tag:blogger.com,1999:blog-604983551614335442024-03-04T23:00:48.144-08:00evolving all we areAnonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.comBlogger1291125tag:blogger.com,1999:blog-60498355161433544.post-75808021039280870012013-11-08T18:23:00.002-08:002013-11-08T18:23:35.523-08:00List of Bioinformatics Workshops and Training Resources<h3 class="post-title entry-title" style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 22px; font-weight: normal; margin: 0.75em 0px 0px; position: relative;">
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<a href="http://gettinggeneticsdone.blogspot.com/2013/04/list-of-bioinformatics-workshops-training.html" style="color: #0074bd; text-decoration: none;">List of Bioinformatics Workshops and Training Resources</a></h3>
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I frequently get asked to recommend workshops or online learning resources for bioinformatics, genomics, statistics, and programming. I <a href="http://stephenturner.us/p/edu" style="color: #0074bd; text-decoration: none;" target="_blank">compiled a list</a> of both online learning resources and in-person workshops (preferentially highlighting those where workshop materials are freely available online):<br /><br /><a href="http://stephenturner.us/p/edu" style="color: #0074bd; text-decoration: none;" target="_blank"><b>List of Bioinformatics Workshops and Training Resources</b></a><br /><br />I hope to keep the page above as up-to-date as possible. Below is a snapshop of what I have listed as of today. Please leave a comment if you're aware of any egregious omissions, and I'll update the page above as appropriate.<br /><br /><i>From <a href="http://stephenturner.us/p/edu" style="color: #0074bd; text-decoration: none;">http://stephenturner.us/p/edu</a>, April 4, 2013</i><br /><b><i><br /></i></b><b><i>In-Person Workshops:</i></b><br /><b><br /></b><b>Cold Spring Harbor Courses: </b><a href="http://meetings.cshl.edu/courses.html" style="color: #0074bd; text-decoration: none;" target="_blank">meetings.cshl.edu/courses.html</a><br /><br />Cold Spring Harbor has been offering advanced workshops and short courses in the life sciences for years. Relevant workshops include <a href="http://meetings.cshl.edu/courses/2013/c-seqtech13.shtml" style="color: #0074bd; text-decoration: none;" title="2013 CSHL course in Advanced Sequencing Technologies & Applications">Advanced Sequencing Technologies & Applications</a>, <a href="http://meetings.cshl.edu/courses/2013/c-ecg13.shtml" style="color: #0074bd; text-decoration: none;" title="2013 CSHL course on Computational & Comparative Genomics">Computational & Comparative Genomics</a>, <a href="http://meetings.cshl.edu/courses/2013/c-info13.shtml" style="color: #0074bd; text-decoration: none;">Programming for Biology</a>, <a href="http://meetings.cshl.edu/courses/2013/c-data13.shtml" style="color: #0074bd; text-decoration: none;" title="2013 CSHL course on Statistical Methods for Functional Genomics">Statistical Methods for Functional Genomics</a>, the <a href="http://meetings.cshl.edu/courses/2013/tgac13.shtml" style="color: #0074bd; text-decoration: none;" title="The Genome Access Course (TGAC) 2013">Genome Access Course</a>, and others. Unlike most of the others below, you won't find material from past years' CSHL courses available online.<br /><b><br /></b><b>Canadian Bioinformatics Workshops: </b><a href="http://bioinformatics.ca/workshops" style="color: #0074bd; text-decoration: none;" target="_blank">bioinformatics.ca/workshops</a><br />Bioinformatics.ca through its Canadian Bioinformatics Workshops (CBW) series began offering one and two week short courses in bioinformatics, genomics and proteomics in 1999. The more recent workshops focus on training researchers using advanced high-throughput technologies on the latest approaches being used in computational biology to deal with the new data. Course material from <a href="http://bioinformatics.ca/workshops/2012" style="color: #0074bd; text-decoration: none;" title="Past Workshops - 2012 | Bioinformatics.ca">past workshops</a> is freely available online, including both audio/video lectures and slideshows. Topics include <a href="http://bioinformatics.ca/workshops/2012/microarray-data-analysis" style="color: #0074bd; text-decoration: none;" title="Microarray Data Analysis | Bioinformatics.ca">microarray analysis</a>, <a href="http://bioinformatics.ca/workshops/2012/informatics-high-throughput-sequencing-data" style="color: #0074bd; text-decoration: none;" title="Informatics on High Throughput Sequencing Data | Bioinformatics.ca">RNA-seq analysis</a>, genome rearrangements, copy number alteration,<a href="http://bioinformatics.ca/workshops/2012/pathway-and-network-analysis-omics-data" style="color: #0074bd; text-decoration: none;" title="Pathway and Network Analysis of -omics Data | Bioinformatics.ca">network/pathway analysis</a>, genome visualization, gene function prediction, functional annotation, data analysis using R, <a href="http://bioinformatics.ca/workshops/2012/informatics-and-statistics-metabolomics" style="color: #0074bd; text-decoration: none;" title="Informatics and Statistics for Metabolomics | Bioinformatics.ca">statistics for metabolomics</a>, and <a href="http://bioinformatics.ca/workshops/2012/informatics-high-throughput-sequencing-data" style="color: #0074bd; text-decoration: none;" title="Informatics on High Throughput Sequencing Data | Bioinformatics.ca">much more</a>.<br /><b><br /></b><b>UC Davis Bioinformatics Training Program: </b><a href="http://training.bioinformatics.ucdavis.edu/" style="color: #0074bd; text-decoration: none;" target="_blank">training.bioinformatics.ucdavis.edu</a><br />The UC Davis Bioinformatics Training program offers several intensive <a href="http://training.bioinformatics.ucdavis.edu/bootcamps/" style="color: #0074bd; text-decoration: none;" title="Boot Camps | UC Davis Bioinformatics Training Program">short bootcamp workshops</a> on RNA-seq, data analysis and visualization, and cloud computing with a focus on Amazon's computing resources. They also offer a week-long <a href="http://training.bioinformatics.ucdavis.edu/courses/" style="color: #0074bd; text-decoration: none;" title="Courses | UC Davis Bioinformatics Training Program">Bioinformatics Short Course</a>, covering in-depth the practical theory and application of cutting-edge next-generation sequencing techniques. Every course's documentation is <a href="http://training.bioinformatics.ucdavis.edu/documentation/" style="color: #0074bd; text-decoration: none;" title="Documentation | UC Davis Bioinformatics Training Program">freely available online</a>, even if you didn't take the course.<br /><b><br /></b><b>MSU NGS Summer Course: </b><a href="http://bioinformatics.msu.edu/ngs-summer-course-2013" style="color: #0074bd; text-decoration: none;" target="_blank">bioinformatics.msu.edu/ngs-summer-course-2013</a><br />This intensive two week summer course will introduce attendees with a strong biology background to the practice of analyzing short-read sequencing data from Illumina and other next-gen platforms. The first week will introduce students to computational thinking and large-scale data analysis on UNIX platforms. The second week will focus on mapping, assembly, and analysis of short-read data for resequencing, ChIP-seq, and RNAseq. <a href="http://ged.msu.edu/angus/" style="color: #0074bd; text-decoration: none;">Materials from previous courses are freely available online</a> under a CC-by-SA license.<br /><b><br /></b><b>Genetic Analysis of Complex Human Diseases: </b><a href="http://hihg.med.miami.edu/educational-programs/analysis-of-complex-human-diseases/genetic-analysis-of-complex-human-diseases/" style="color: #0074bd; text-decoration: none;" target="_blank">hihg.med.miami.edu/edu...</a><br />The Genetic Analysis of Complex Human Diseases is a comprehensive four-day course directed toward physician-scientists and other medical researchers. The course will introduce state-of-the-art approaches for the mapping and characterization of human inherited disorders with an emphasis on the mapping of genes involved in common and genetically complex disease phenotypes. The primary goal of this course is to provide participants with an overview of approaches to identifying genes involved in complex human diseases. At the end of the course, participants should be able to identify the key components of a study team, and communicate effectively with specialists in various areas to design and execute a study. The course is in Miami Beach, FL. (Full Disclosure: I teach a section in this course.) Most of the course material from previous years is not available online, but <a href="http://figshare.com/authors/Stephen%20Turner/100774" style="color: #0074bd; text-decoration: none;" title="Stephen Turner">my RNA-seq & methylation lectures are on Figshare</a>.<br /><b><br /></b><b>UAB Short Course on Statistical Genetics and Genomics: </b><a href="http://www.soph.uab.edu/ssg/nigmsstatgen/third" style="color: #0074bd; text-decoration: none;" target="_blank">soph.uab.edu/ssg/...</a><br />Focusing on the state-of-art methodology to analyze complex traits, this five-day course will offer an interactive program to enhance researchers' ability to understand & use statistical genetic methods, as well as implement & interpret sophisticated genetic analyses. Topics include GWAS Design/Analysis/Imputation/Interpretation; Non-Mendelian Disorders Analysis; Pharmacogenetics/Pharmacogenomics; ELSI; Rare Variants & Exome Sequencing; Whole Genome Prediction; Analysis of DNA Methylation Microarray Data; Variant Calling from NGS Data; RNAseq: Experimental Design and Data Analysis; Analysis of ChIP-seq Data; Statistical Methods for NGS Data; Discovering new drugs & diagnostics from 300 billion points of data. Video recording from the 2012 course are <a href="http://www.soph.uab.edu/ssg/nigmsstatgen/second" style="color: #0074bd; text-decoration: none;" title="2nd Short Course on Statistical Genetics and Genomics | Section on Statistical Genetics">available online</a>.<br /><b><br /></b><b>MBL Molecular Evolution Workshop: </b><a href="http://hermes.mbl.edu/education/courses/special_topics/mole.html" style="color: #0074bd; text-decoration: none;" target="_blank">hermes.mbl.edu/education/...</a><br />One of the longest-running courses listed here (est. 1988), the Workshop on Molecular Evolution at Woods Hole presents a series of lectures, discussions, and bioinformatic exercises that span contemporary topics in molecular evolution. The course addresses phylogenetic analysis, population genetics, database and sequence matching, molecular evolution and development, and comparative genomics, <a href="https://molevol.mbl.edu/wiki/index.php/Software" style="color: #0074bd; text-decoration: none;">using software packages</a> including AWTY, BEAST, BEST, Clustal W/X, FASTA, FigTree, GARLI, MIGRATE, LAMARC, MAFFT, MP-EST, MrBayes, PAML, PAUP*, PHYLIP, STEM, STEM-hy, and SeaView. Some of the course materials can be found by digging around the <a href="https://molevol.mbl.edu/wiki/index.php/Main_Page" style="color: #0074bd; text-decoration: none;">course wiki</a>.<br /><b><i><br /></i></b><b><i><br class="Apple-interchange-newline" />Online Material:</i></b><br /><br /><b>Canadian Bioinformatics Workshops: </b><a href="http://bioinformatics.ca/workshops" style="color: #0074bd; text-decoration: none;" target="_blank">bioinformatics.ca/workshops</a><br />(<i>In person workshop described above</i>). Course material from <a href="http://bioinformatics.ca/workshops/2012" style="color: #0074bd; text-decoration: none;" title="Past Workshops - 2012 | Bioinformatics.ca">past workshops</a> is freely available online, including both audio/video lectures and slideshows. Topics include <a href="http://bioinformatics.ca/workshops/2012/microarray-data-analysis" style="color: #0074bd; text-decoration: none;" title="Microarray Data Analysis | Bioinformatics.ca">microarray analysis</a>, <a href="http://bioinformatics.ca/workshops/2012/informatics-high-throughput-sequencing-data" style="color: #0074bd; text-decoration: none;" title="Informatics on High Throughput Sequencing Data | Bioinformatics.ca">RNA-seq analysis</a>, genome rearrangements, copy number alteration, <a href="http://bioinformatics.ca/workshops/2012/pathway-and-network-analysis-omics-data" style="color: #0074bd; text-decoration: none;" title="Pathway and Network Analysis of -omics Data | Bioinformatics.ca">network/pathway analysis</a>, genome visualization, gene function prediction, functional annotation, data analysis using R, <a href="http://bioinformatics.ca/workshops/2012/informatics-and-statistics-metabolomics" style="color: #0074bd; text-decoration: none;" title="Informatics and Statistics for Metabolomics | Bioinformatics.ca">statistics for metabolomics</a>, and<a href="http://bioinformatics.ca/workshops/2012/informatics-high-throughput-sequencing-data" style="color: #0074bd; text-decoration: none;" title="Informatics on High Throughput Sequencing Data | Bioinformatics.ca">much more</a>.<br /><b><br /></b><b>UC Davis Bioinformatics Training Program: </b><a href="http://training.bioinformatics.ucdavis.edu/" style="color: #0074bd; text-decoration: none;" target="_blank">training.bioinformatics.ucdavis.edu</a><br />(<i>In person workshop described above</i>). Every course's documentation is <a href="http://training.bioinformatics.ucdavis.edu/documentation/" style="color: #0074bd; text-decoration: none;" title="Documentation | UC Davis Bioinformatics Training Program">freely available online</a>, even if you didn't take the course. <a href="http://training.bioinformatics.ucdavis.edu/documentation/" style="color: #0074bd; text-decoration: none;" title="Documentation | UC Davis Bioinformatics Training Program">Past topics</a> include Galaxy, Bioinformatics for NGS, cloud computing, and RNA-seq.<br /><b><br /></b><b>MSU NGS Summer Course: </b><a href="http://bioinformatics.msu.edu/ngs-summer-course-2013" style="color: #0074bd; text-decoration: none;" target="_blank">bioinformatics.msu.edu/ngs-summer-course-2013</a><br />(<i>In person workshop described above</i>). <a href="http://ged.msu.edu/angus/" style="color: #0074bd; text-decoration: none;">Materials from previous courses are freely available online</a> under a CC-by-SA license, which cover mapping, assembly, and analysis of short-read data for resequencing, ChIP-seq, and RNAseq.<br /><b><br /></b><b>EMBL-EBI Train Online: </b><a href="http://www.ebi.ac.uk/training/online/" style="color: #0074bd; text-decoration: none;" target="_blank">www.ebi.ac.uk/training/online</a><br />Train online provides free courses on Europe's most widely used data resources, created by experts at EMBL-EBI and collaborating institutes. Topics include <a href="http://www.ebi.ac.uk/training/online/subjects/11" style="color: #0074bd; text-decoration: none;" title="Train online courses | Train online">Genes and Genomes</a>, <a href="http://www.ebi.ac.uk/training/online/subjects/13" style="color: #0074bd; text-decoration: none;" title="Train online courses | Train online">Gene Expression</a>,<a href="http://www.ebi.ac.uk/training/online/subjects/479" style="color: #0074bd; text-decoration: none;" title="Train online courses | Train online">Interactions, Pathways, and Networks</a>, and others. Of particular interest may be the <a href="http://www.ebi.ac.uk/training/online/course/embo-practical-course-analysis-high-throughput-seq" style="color: #0074bd; text-decoration: none;" title="EMBO Practical Course on Analysis of High-Throughput Sequencing Data | Train online">Practical Course on Analysis of High-Throughput Sequencing Data</a>, which covers Bioconductor packages for short read analysis, ChIP-Seq, RNA-seq, and allele-specific expression & eQTLs.<br /><b><br /></b><b>UC Riverside Bioinformatics Manuals: </b><a href="http://manuals.bioinformatics.ucr.edu/" style="color: #0074bd; text-decoration: none;" target="_blank">manuals.bioinformatics.ucr.edu</a><br />This is an excellent collection of manuals and code snippets. Topics include <a href="http://manuals.bioinformatics.ucr.edu/home/programming-in-r" style="color: #0074bd; text-decoration: none;" title="R Programming - Manuals">Programming in R</a>, <a href="http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual" style="color: #0074bd; text-decoration: none;" title="R and Bioconductor - Manuals">R+Bioconductor</a>, <a href="http://manuals.bioinformatics.ucr.edu/home/ht-seq" style="color: #0074bd; text-decoration: none;" title="NG Sequence - Manuals">Sequence Analysis with R and Bioconductor</a>, <a href="http://manuals.bioinformatics.ucr.edu/home/gui-ngs-analysis" style="color: #0074bd; text-decoration: none;" title="NGS GUI - Manuals">NGS analysis with Galaxy and IGV</a>, basic<a href="http://manuals.bioinformatics.ucr.edu/home/linux-basics" style="color: #0074bd; text-decoration: none;" title="Linux Basics - Manuals">Linux skills</a>, and others.<br /><b><br /></b><b>Software Carpentry: </b><a href="http://software-carpentry.org/" style="color: #0074bd; text-decoration: none;" target="_blank">software-carpentry.org</a><br />Software Carpentry helps researchers be more productive by teaching them basic computing skills. We recently ran a <a href="http://gettinggeneticsdone.blogspot.com/2013/03/software-carpentry-bootcamp-at.html" style="color: #0074bd; text-decoration: none;">2-day Software Carpentry Bootcamp here at UVA</a>. Check out the <a href="http://software-carpentry.org/4_0/index.html" style="color: #0074bd; text-decoration: none;">online lectures</a> for some introductory material on Unix, Python, Version Control, Databases, Automation, and many other topics.<br /><b><br /></b><b>Coursera: </b><a href="https://www.coursera.org/courses" style="color: #0074bd; text-decoration: none;" target="_blank">coursera.org/courses</a><br />Coursera partners with top universities to offer courses online for anytone to take, for free. Courses are usually 4-6 weeks, and consist of video lectures, quizzes, assignments, and exams. Joining a course gives you access to the course's forum where you can interact with the instructor and other participants. Relevant courses include <a href="https://www.coursera.org/course/dataanalysis" style="color: #0074bd; text-decoration: none;">Data Analysis</a>, <a href="https://www.coursera.org/course/compdata" style="color: #0074bd; text-decoration: none;">Computing for Data Analysis using R</a>, and <a href="https://www.coursera.org/course/bioinformatics" style="color: #0074bd; text-decoration: none;">Bioinformatics Algorithms</a>, among others. You can also <a href="http://www.youtube.com/user/jtleek2007/videos?flow=grid&tag_id=UC8xNPQ-3a5t9uMU7Vah-jWA.3.coursera&view=46" style="color: #0074bd; text-decoration: none;" title="Jeff Leek - YouTube">view all of Jeff Leek's Data Analysis lectures on Youtube</a>.<br /><b>Rosalind: </b><a href="http://rosalind.info/" style="color: #0074bd; text-decoration: none;" target="_blank">http://rosalind.info</a><br />Quite different from the others listed here, Rosalind is a platform for learning bioinformatics through gaming-like problem solving. Visit the <a href="http://rosalind.info/problems/list-view/?location=python-village" style="color: #0074bd; text-decoration: none;" target="_blank" title="ROSALIND | Problems">Python Village</a> to learn the basics of Python. Arm yourself at the<a href="http://rosalind.info/problems/list-view/?location=bioinformatics-armory" style="color: #0074bd; text-decoration: none;" target="_blank" title="ROSALIND | Problems">Bioinformatics Armory</a>, equipping yourself with existing ready-to-use bioinformatics software tools. Or storm the <a href="http://rosalind.info/problems/list-view/" style="color: #0074bd; text-decoration: none;" target="_blank" title="ROSALIND | Problems">Bioinformatics Stronghold</a>, implementing your own algorithms for computational mass spectrometry, alignment, dynamic programming, genome assembly, genome rearrangements, phylogeny, probability, string algorithms and others.<br /><br /><b><i><br class="Apple-interchange-newline" />Other Resources:</i></b><br /><br /><ul style="line-height: 1.4; margin: 0.5em 0px; padding: 0px 2.5em;">
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://ged.msu.edu/angus/bioinformatics-courses.html" style="color: #0074bd; text-decoration: none;" target="_blank" title="A list of bioinformatics courses — ANGUS 2.0 documentation">Titus Brown's list bioinformatics courses</a>: Includes a few others not listed here (also see the comments).</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://gmod.org/wiki/Training_and_Outreach" style="color: #0074bd; text-decoration: none;" target="_blank" title="Training and Outreach - GMOD">GMOD Training and Outreach</a>: GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases. This page links out to tutorials on <a href="http://gmod.org/wiki/GMOD_Components" style="color: #0074bd; text-decoration: none;" title="GMOD Components - GMOD">GMOD Components</a> such as Apollo, BioMart, Galaxy, GBrowse, MAKER, and others.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://seqanswers.com/" style="color: #0074bd; text-decoration: none;" target="_blank" title="SEQanswers Home">Seqanswers.com</a>: A discussion forum for anything related to Bioinformatics, including Q&A, paper discussions, new software announcements, protocols, and more.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://www.biostars.org/" style="color: #0074bd; text-decoration: none;" target="_blank" title="Bioinformatics Answers">Biostars.org</a>: Similar to SEQanswers, but more strictly a Q&A site.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://www.bioconductor.org/help/mailing-list/" style="color: #0074bd; text-decoration: none;" target="_blank" title="Bioconductor - Mailing Lists">BioConductor Mailing list</a>: A very active mailing list for getting help with Bioconductor packages. Make sure you do some Google searching yourself first before posting to this list.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://www.bioconductor.org/help/events/" style="color: #0074bd; text-decoration: none;" target="_blank" title="Bioconductor - Events">Bioconductor Events</a>: List of upcoming and prior Bioconductor training and events worldwide.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://wiki.galaxyproject.org/Learn" style="color: #0074bd; text-decoration: none;" target="_blank" title="Learn - Galaxy Wiki">Learn Galaxy</a>: Screencasts and tutorials for learning to use Galaxy.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://wiki.galaxyproject.org/Events" style="color: #0074bd; text-decoration: none;" target="_blank" title="Events - Galaxy Wiki">Galaxy Event Horizon</a>: Worldwide Galaxy-related events (workshops, training, user meetings) are listed here.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise" style="color: #0074bd; text-decoration: none;" target="_blank">Galaxy RNA-Seq Exercise</a>: Run through a small RNA-seq study from start to finish using Galaxy.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://www.youtube.com/user/RafalabChannel" style="color: #0074bd; text-decoration: none;" target="_blank" title="Rafael Irizarry - YouTube">Rafael Irizarry's Youtube Channel</a>: Several statistics and bioinformatics video lectures.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002632" style="color: #0074bd; text-decoration: none;" target="_blank" title="PLOS Computational Biology: An Online Bioinformatics Curriculum">PLoS Comp Bio Online Bioinformatics Curriculum</a>: A perspective paper by David B Searls outlining a series of free online learning initiatives for beginning to advanced training in biology, biochemistry, genetics, computational biology, genomics, math, statistics, computer science, programming, web development, databases, parallel computing, image processing, AI, NLP, and more.</li>
<li style="margin: 0px 0px 0.25em; padding: 0px;"><a href="http://gettinggeneticsdone.blogspot.com/" style="color: #0074bd; text-decoration: none;" target="_blank" title="Getting Genetics Done">Getting Genetics Done</a>: Shameless plug – I write a blog highlighting literature of interest, new tools, and occasionally tutorials in genetics, statistics, and bioinformatics. I recently wrote <a href="http://gettinggeneticsdone.blogspot.com/2012/05/how-to-stay-current-in.html" style="color: #0074bd; text-decoration: none;" title="Getting Genetics Done: How to Stay Current in Bioinformatics/Genomics">this post about how to stay current in bioinformatics & genomics</a>.</li>
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Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-80998122224367251612013-11-08T01:02:00.001-08:002013-11-08T01:02:38.101-08:00A Mitochondrial Manhattan Plot<h3 class="post-title entry-title" style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 22px; font-weight: normal; margin: 0.75em 0px 0px; position: relative;">
A Mitochondrial Manhattan Plot</h3>
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Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-41259084457300857642013-11-08T00:56:00.002-08:002013-11-08T00:58:03.411-08:00Lior Pachter's lab<a href="http://math.berkeley.edu/~lpachter/software.html">http://math.berkeley.edu/~lpachter/software.html</a><br />
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<dl style="background-color: white; font-family: Candara, 'News Gothic MT', 'Bitstream Vera Sans', Verdana, Trebuchet, 'Trebuchet MS', sans-serif; font-size: 15px; line-height: 20px;">
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">Software developed in the Pachter group and still under active development in the group</dt>
<ul>
<li><a href="http://bio.math.berkeley.edu/eXpress/" style="color: blue;">eXpress</a> (2012) Streaming quantification for high-throughput sequencing.</li>
<li><a href="http://bio.math.berkeley.edu/SysCall/" style="color: blue;">SysCall</a> (2011) Distinguishing heterozygous sites from systematic error in high-thoughput sequenced reads</li>
<li><a href="http://cufflinks.cbcb.umd.edu/" style="color: blue;">Cufflinks</a> (2010) Transcript assembly and abundance estimation for RNA-Seq (now a joint effort together with <a href="http://www.broadinstitute.org/~cole/" style="color: blue;">Cole Trapnell</a> and the <a href="http://www.rinnlab.com/" style="color: blue;">John Rinn Lab</a> at Harvard University)</li>
<li><a href="http://www.cs.berkeley.edu/~meromit/MetMap.html" style="color: blue;">MetMap</a> (2010) Analysis of Methyl-Seq experiments</li>
</ul>
</dl>
<dl style="background-color: white; font-family: Candara, 'News Gothic MT', 'Bitstream Vera Sans', Verdana, Trebuchet, 'Trebuchet MS', sans-serif; font-size: 15px; line-height: 20px;">
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">Software developed in the Pachter group but now maintained/developed elsewhere</dt>
<ul>
<li><a href="http://www.math.miami.edu/~vhower/ReadSpy.html" style="color: blue;">ReadSpy</a> (2012) Assessment of uniformity in RNA-Seq reads (now supported by <a href="http://www.math.miami.edu/~vhower/" style="color: blue;">Valerie Hower</a> and her group at the University of Miami)</li>
<li><a href="http://tophat.cbcb.umd.edu/" style="color: blue;">TopHat</a> (2009) Splice junction mapper for short RNA-seq reads (now supported by <a href="http://bioinformatics.igm.jhmi.edu/salzberg/Salzberg/Salzberg_Lab_Home.html" style="color: blue;">Steven Salzberg</a> and his group at Johns Hopkins University)</li>
<li><a href="http://orangutan.math.berkeley.edu/fsa/" style="color: blue;">FSA</a> (2009) <b>F</b>ast <b>S</b>tatistical <b>A</b>lignment (now supported by <a href="http://labs.fhcrc.org/bradleyr/" style="color: blue;">Robert Bradley</a> and his group at FHCRC)</li>
<li><a href="http://www.biostat.wisc.edu/~cdewey/mercator/" style="color: blue;">MERCATOR</a> (2004) Homology mapping (now supported by <a href="http://www.biostat.wisc.edu/~cdewey/" style="color: blue;">Colin Dewey</a> and his group at the University of Wisconsin)</li>
<li><a href="http://genome.lbl.gov/vista/mvista/about.shtml" style="color: blue;">VISTA</a> (2000) Visualization tool for global alignments (now supported by <a href="http://www.jgi.doe.gov/whoweare/dubchak.html" style="color: blue;">Inna Dubchak</a> and her group at the JGI)</li>
</ul>
</dl>
<dl style="background-color: white; font-family: Candara, 'News Gothic MT', 'Bitstream Vera Sans', Verdana, Trebuchet, 'Trebuchet MS', sans-serif; font-size: 15px; line-height: 20px;">
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">Retired Software</dt>
These programs, originally developed in the Pachter group, are no longer under active development and are not being supported.<ul>
<li><u>AMAP</u> (2007) Protein multiple alignment (recommended instead: <a href="http://orangutan.math.berkeley.edu/fsa/" style="color: blue;">FSA</a>)</li>
<li><u>GENEMAPPER</u> (2006) Reference based gene annotation (recommended instead: <a href="http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html" style="color: blue;">an RNA-Seq experiment</a>)</li>
<li><u>MJOIN</u> (2006) Neighbor joining with subtree weights (archived <a href="http://bio.math.berkeley.edu/mjoin/" style="color: blue;">here</a>)</li>
<li><u>PARALIGN</u> (2006) Alignment polytope construction (archived <a href="http://bio.math.berkeley.edu//paralign/" style="color: blue;">here</a>)</li>
<li><u>SLIM</u> (2003) Minimum network design for optimizing the search space for pair hidden Markov models (archived <a href="http://bio.math.berkeley.edu/slim/" style="color: blue;">here</a>)</li>
<li><u>SLAM</u> (2003) Pairwise simultaneous alignment and gene finding (recommended instead: <a href="http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html" style="color: blue;">an RNA-Seq experiment</a>)</li>
<li><u>MAVID</u> (2003) Multiple alignment of large genomic sequences (recommended instead: <a href="http://orangutan.math.berkeley.edu/fsa/" style="color: blue;">FSA</a>)</li>
</ul>
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<dl>
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">################################################################################</dt>
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">Submitted</dt>
<dd style="margin-left: 10px;">L. Pachter, <a href="http://arxiv.org/abs/1104.3889" style="color: blue;"><b>Models for transcript quantification from RNA-Seq</b></a>, submitted.</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
</dl>
<dl>
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">In press</dt>
<dd style="margin-left: 10px;">A. Roberts, L. Schaeffer and L. Pachter, <b>Updating RNA-Seq analyses after re-annotation</b>, in press.</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
<dd style="margin-left: 10px;">M. Singer and L. Pachter, <b>Bayesian networks in the study of genomewide DNA methylation</b>, in press.</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
</dl>
<dl>
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">2013</dt>
<dd style="margin-left: 10px;">A. Rahman and L. Pachter, <a href="http://genomebiology.com/2013/14/1/R8/abstract" style="color: blue;"><b>CGAL: computing genome assembly likelihoods</b></a>, Genome Biology, 14 (2013), R8.</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
</dl>
<dl>
<dt style="border-bottom-color: rgb(204, 204, 204); border-bottom-style: solid; border-bottom-width: 1px; font-weight: bold;">2012</dt>
<dd style="margin-left: 10px;">C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn and L. Pachter, <a href="http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.2450.html" style="color: blue;"><b>Differential analysis of gene regulation at transcript resolution with RNA-seq</b></a>, Nature Biotechnology, advance online publication (2012).</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
<dd style="margin-left: 10px;">S.A. Mortimer, C. Trapnell, S. Aviran, L. Pachter and J.B. Lucks, <a href="http://onlinelibrary.wiley.com/doi/10.1002/9780470559277.ch120019/abstract" style="color: blue;"><b>SHAPE-Seq: High throughput RNA structure analysis</b></a>, Current Protocols in Chemical Biology, advance online publication.</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
<dd style="margin-left: 10px;">A. Kleinman, M. Harel and L. Pachter, <a href="http://link.springer.com/article/10.1007/s00026-012-0173-2" style="color: blue;"><b>Affine and projective tree metric theorems</b></a>, Annals of Combinatorics, advance online publication (2012).</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
<dd style="margin-left: 10px;">A. Roberts and L. Pachter, <a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2251.html" style="color: blue;"><b>Streaming fragment assignment for real-time analysis of sequencing experiments</b></a>, Nature Methods, advance online publication (2012).</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
<dd style="margin-left: 10px;">V. Hower, R. Starfield, A. Roberts, and L. Pachter, <b><a href="http://bioinformatics.oxfordjournals.org/content/28/20/2680.long" style="color: blue;">Quantifying uniformity in mapped reads</a></b>, Bioinformatics, 28 (2012), 2680--2682.</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
<dd style="margin-left: 10px;">L. Pachter, <a href="http://www.nature.com/nbt/journal/v30/n3/pdf/nbt.2156.pdf" style="color: blue;"><b>A closer look at RNA editing</b></a>, Nature Biotechnology, 30 (2012), 246--247.</dd><div style="letter-spacing: 0.01em; line-height: 1.5;">
</div>
<dd style="margin-left: 10px;">C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimentel, S.L. Salzberg, J.L. Rinn and L. Pachter, <a href="http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html" style="color: blue;"><b>Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks</b></a>, Nature Protocols, 7 (2012), 562--578.</dd></dl>
</div>
</dl>
Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-1646911485898285972013-11-08T00:40:00.002-08:002013-11-08T00:42:18.791-08:00SysCall - Distinguishing heterozygous sites from systematic errors<a href="http://bio.math.berkeley.edu/SysCall/">http://bio.math.berkeley.edu/SysCall/</a><br />
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<span 0="" 51="" color:="" rgb="" style="color: #003300; font-size: 19px;">SysCall is a logistic regression based classifier.<br />Given a list of candidate heterozygous genomic locations and a sam file of sequenced reads SysCall classifies each genomic location as either a heterozygous site or a systematic error and outputs according lists, along with the assigned posterior probabilities.<br /><br />The submitted manuscript describing SysCall can be found <a href="http://precedings.nature.com/documents/5989/version/1">here</a> and the lists of systematic errors reported in the paper are <a href="http://bio.math.berkeley.edu/SysCall/systematic_error_lists/">here </a>.<br />The slides from a talk on SysCall given at the 2011 CSHL Meeting on The Biology of Genomes can be found <a href="http://www.cs.berkeley.edu/~meromit/sys_csh2011.key">here</a>. </span><span style="color: #000099; font-size: 19px;"></span><br />
<span 0="" 51="" color:="" rgb="" style="color: #003300; font-size: 19px;"><br /></span>
<span 0="" 51="" color:="" rgb="" style="color: #003300; font-size: 19px;"><span style="color: #006300;"><span style="font-weight: bold;">Manual </span></span><span style="color: #000099;"></span>Click here to download the <a href="http://www.cs.berkeley.edu/~meromit/SysCall_manual.pdf">SysCall manual</a>.</span><br />
<span 0="" 51="" color:="" rgb="" style="color: #003300; font-size: 19px;"><br /></span>
<span 0="" 51="" color:="" rgb="" style="background-color: #38761d; color: white; font-size: 19px;">Paper</span><br />
<span 0="" 51="" color:="" rgb="" style="color: #003300; font-size: 19px;"><a href="http://www.biomedcentral.com/1471-2105/12/451/">http://www.biomedcentral.com/1471-2105/12/451/</a></span>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-71514171273990449422013-11-08T00:34:00.002-08:002013-11-08T00:34:40.411-08:00PubMed Commons: One post-publication peer review forum to rule them all?<a href="http://gettinggeneticsdone.blogspot.com/2013/10/pubmed-commons-post-publication-peer-review.html">http://gettinggeneticsdone.blogspot.com/2013/10/pubmed-commons-post-publication-peer-review.html</a>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-91389924031506677712013-11-08T00:32:00.000-08:002013-11-08T00:32:50.771-08:00Useful Unix/Linux One-Liners for Bioinformatics<a href="http://gettinggeneticsdone.blogspot.com/2013/10/useful-linux-oneliners-for-bioinformatics.html">http://gettinggeneticsdone.blogspot.com/2013/10/useful-linux-oneliners-for-bioinformatics.html</a><br />
<br />
<span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">Much of the work that bioinformaticians do is munging and wrangling around massive amounts of text. While there are some "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.), there are still times where knowing a little bit of Unix/Linux is extremely helpful, namely awk, sed, cut, grep, GNU parallel, and others.</span><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">This is by no means an exhaustive catalog, but I've put together a </span><a href="https://github.com/stephenturner/oneliners" style="background-color: white; color: #0074bd; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px; text-decoration: none;" target="_blank">short list of examples using various Unix/Linux utilities for text manipulation</a><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">, from the very basic (e.g., sum a column) to the very advanced (munge a FASTQ file and print the total number of reads, total number unique reads, percentage of unique reads, most abundant sequence, and its frequency). Most of these examples (with the exception of the SeqTK examples) use built-in utilities installed on nearly every Linux system. These examples are a combination of tactics I used everyday and examples culled from other sources listed at the top of the page.</span><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><br />
<div class="separator" style="background-color: white; clear: both; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px; text-align: center;">
<a href="https://github.com/stephenturner/oneliners" imageanchor="1" style="color: #0074bd; margin-left: 1em; margin-right: 1em; text-decoration: none;" target="_blank"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiN1q-6fqfuEmnNdZuHrPZdfRHwuN8VJF8aAErZzjj9WcdRd8GHOo1U4eHPOCdOnU5_2pFCUaPFRaGcklUUViwBw4F3RzGQeEmdDnmMUkBnV76lMLur1yP_219iuvyM3EgR_MYNhmi2dA/s1600/oneliners.png" style="-webkit-box-shadow: transparent 0px 0px 0px !important; background-image: none !important; background-position: initial initial !important; background-repeat: initial initial !important; border: none !important; box-shadow: transparent 0px 0px 0px !important; padding: 5px; position: relative;" /></a></div>
<br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">The list is available as a </span><a href="https://github.com/stephenturner/oneliners" style="background-color: white; color: #0074bd; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px; text-decoration: none;" target="_blank">README in this GitHub repo</a><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">. This list is a start - I would love suggestions for other things to include. To make a suggestion, leave a comment here, or better - </span><a href="https://github.com/stephenturner/oneliners/issues" style="background-color: white; color: #0074bd; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px; text-decoration: none;" target="_blank">open an issue</a><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">, or even better still - send me a </span><a href="https://help.github.com/articles/using-pull-requests" style="background-color: white; color: #0074bd; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px; text-decoration: none;" target="_blank">pull request</a><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">.</span><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">Useful one-liners for bioinformatics: </span><a href="https://github.com/stephenturner/oneliners" style="background-color: white; color: #0074bd; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px; text-decoration: none;">https://github.com/stephenturner/oneliners</a><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><br style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;" /><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">Alternatively, download a </span><a href="https://github.com/stephenturner/oneliners/blob/master/README.md.pdf?raw=true" style="background-color: white; color: #0074bd; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px; text-decoration: none;" target="_blank">PDF here</a><span style="background-color: white; color: #666666; font-family: 'Trebuchet MS', Trebuchet, Verdana, sans-serif; font-size: 13px; line-height: 18px;">.</span>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-27121953443473842322013-11-08T00:27:00.000-08:002013-11-08T00:27:10.350-08:00De Novo Transcriptome Assembly with Trinity: Protocol and Videos<a href="http://gettinggeneticsdone.blogspot.com/2013/10/de-novo-transcriptome-assembly-trinity.html">http://gettinggeneticsdone.blogspot.com/2013/10/de-novo-transcriptome-assembly-trinity.html</a><br />
<br />
<br />Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-63073068240926530272013-10-02T00:25:00.003-07:002013-10-02T00:25:30.040-07:00two tools - for detecting the genetic basis of adaptation1. <span style="background-color: white; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 14px; font-weight: bold; line-height: 14px;">DISENTANGLING THE EFFECTS OF GEOGRAPHIC AND ECOLOGICAL ISOLATION ON GENETIC DIFFERENTIATION</span><br />
<span style="background-color: white; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 14px; font-weight: bold; line-height: 14px;"><br /></span>
<a href="http://onlinelibrary.wiley.com/doi/10.1111/evo.12193/full">http://onlinelibrary.wiley.com/doi/10.1111/evo.12193/full</a><br />
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<span style="background-color: #e9eff0; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px;">Populations can be genetically isolated both by geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the relative contributions of geographic distance and ecological distance to genetic differentiation between sampled populations or individuals. We model the allele frequencies in a set of populations at a set of unlinked loci as spatially correlated Gaussian processes, in which the covariance structure is a decreasing function of both geographic and ecological distance. Parameters of the model are estimated using a Markov chain Monte Carlo algorithm. We call this method Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology (BEDASSLE), and have implemented it in a user-friendly format in the statistical platform R. We demonstrate its utility with a simulation study and empirical applications to human and teosinte data sets.</span><br />
<span style="background-color: #e9eff0; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px;"><br /></span>
<a href="http://genescape.ucdavis.edu/scripts-and-code/">http://genescape.ucdavis.edu/scripts-and-code/</a><br />
<br />
2. <span style="background-color: white; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 14px; font-weight: bold; line-height: 14px;">INTEGRATING LANDSCAPE GENOMICS AND SPATIALLY EXPLICIT APPROACHES TO DETECT LOCI UNDER SELECTION IN CLINAL POPULATIONS</span><br />
<span style="background-color: white; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 14px; font-weight: bold; line-height: 14px;"><br /></span>
<a href="http://onlinelibrary.wiley.com/doi/10.1111/evo.12237/abstract">http://onlinelibrary.wiley.com/doi/10.1111/evo.12237/abstract</a><br />
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<span style="background-color: white; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px;">Uncovering the genetic basis of adaptation hinges on the ability to detect loci under selection. However, population genomics outlier approaches to detect selected loci may be inappropriate for clinal populations or those with unclear population structure because they require that individuals be clustered into populations. An alternate approach, landscape genomics, uses individual-based approaches to detect loci under selection and reveal potential environmental drivers of selection. We tested four landscape genomics methods on a simulated clinal population to determine their effectiveness at identifying a locus under varying selection strengths along an environmental gradient. We found all methods produced very low type I error rates across all selection strengths, but elevated type II error rates under “weak” selection. We then applied these methods to an AFLP genome scan of an alpine plant, </span><em style="background-color: white; border: 0px; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Campanula barbata</em><span style="background-color: white; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px;">, and identified five highly supported candidate loci associated with precipitation variables. These loci also showed spatial autocorrelation and cline patterns indicative of selection along a precipitation gradient. Our results suggest that landscape genomics in combination with other spatial analyses provides a powerful approach for identifying loci potentially under selection and explaining spatially complex interactions between species and their environment.</span><br />
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<span style="background-color: white; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px;"><br /></span>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-91841597620351772812013-10-01T22:32:00.001-07:002013-10-01T22:32:14.089-07:00Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes<span style="background-color: white; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; text-align: justify;">Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of </span><em style="background-color: white; border: 0px; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; margin: 0px; outline-style: none; padding: 0px; text-align: justify; vertical-align: baseline;">Arabidopsis thaliana</em><span style="background-color: white; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; text-align: justify;"> and </span><em style="background-color: white; border: 0px; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; margin: 0px; outline-style: none; padding: 0px; text-align: justify; vertical-align: baseline;">Vitis vinifera</em><span style="background-color: white; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; text-align: justify;">; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of </span><em style="background-color: white; border: 0px; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; margin: 0px; outline-style: none; padding: 0px; text-align: justify; vertical-align: baseline;">Brachypodium distachyon</em><span style="background-color: white; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; text-align: justify;"> and </span><em style="background-color: white; border: 0px; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; margin: 0px; outline-style: none; padding: 0px; text-align: justify; vertical-align: baseline;">Oryza sativa</em><span style="background-color: white; color: #403838; font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; font-size: 13px; line-height: 19px; text-align: justify;">, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.</span><br />
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<a href="http://genome.cshlp.org/content/22/12/2455.long">http://genome.cshlp.org/content/22/12/2455.long</a><br />
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<span style="background-color: white; line-height: 19px; text-align: justify;"><span style="color: #403838; font-family: Lucida Sans Unicode, Arial, Lucida Grande, Tahoma, Verdana, Helvetica, sans-serif; font-size: x-small;"><br /></span></span>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-44829858127617289502013-09-28T02:10:00.000-07:002013-09-28T02:10:46.405-07:00ngsplot - mining and visualization of next-generation sequencing data by integrating genomic databases<br />
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<a href="https://ngsplot.googlecode.com/files/k4_bampair.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="197" src="https://ngsplot.googlecode.com/files/k4_bampair.png" width="320" /></a></div>
<a href="http://code.google.com/p/ngsplot/">http://code.google.com/p/ngsplot/</a><br />Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-57687707863839428282013-09-22T21:38:00.001-07:002013-09-22T21:38:48.988-07:00Population genomics from pool sequencing<div class="keywords" style="background-color: white; border: 0px; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 10px; margin: 0px 0px 1em; outline: 0px; overflow: hidden; padding: 0px; vertical-align: baseline;">
<h3 class="keywordsHeading" style="background-color: transparent; border: 0px; float: left; font-size: 1.2em; line-height: 14px; margin: 0.2em 0.5em 0px 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
Keywords:</h3>
<div class="keywordLists" style="background-color: transparent; border: 0px; float: left; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
<ul class="keywordList" id="abstractKeywords1" style="background-color: transparent; border: 0px; list-style: none; margin: 0px; outline: 0px; overflow: hidden; padding: 0px; vertical-align: baseline; width: 72.3em;">
<li style="background-color: transparent; background-position: initial initial; background-repeat: initial initial; border: 0px; display: inline; font-size: 1.2em; line-height: 1.5em; margin: 0px; outline: 0px; padding: 0px 0.3em 0px 0px; vertical-align: baseline;">Pool sequencing;</li>
<li style="background-color: transparent; background-position: initial initial; background-repeat: initial initial; border: 0px; display: inline; font-size: 1.2em; line-height: 1.5em; margin: 0px; outline: 0px; padding: 0px 0.3em 0px 0px; vertical-align: baseline;">High throughput sequencing;</li>
<li style="background-color: transparent; background-position: initial initial; background-repeat: initial initial; border: 0px; display: inline; font-size: 1.2em; line-height: 1.5em; margin: 0px; outline: 0px; padding: 0px 0.3em 0px 0px; vertical-align: baseline;">Neutrality tests;</li>
<li style="background-color: transparent; background-position: initial initial; background-repeat: initial initial; border: 0px; display: inline; font-size: 1.2em; line-height: 1.5em; margin: 0px; outline: 0px; padding: 0px 0.3em 0px 0px; vertical-align: baseline;">Composite likelihood estimators;</li>
<li style="background-color: transparent; background-position: initial initial; background-repeat: initial initial; border: 0px; display: inline; font-size: 1.2em; line-height: 1.5em; margin: 0px; outline: 0px; padding: 0px 0.3em 0px 0px; vertical-align: baseline;">Genetic differentiation</li>
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<div id="abstract" style="background-color: white; border: 0px; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 10px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
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Abstract</h3>
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Next generation sequencing of pooled samples is an effective approach for studies of variability and differentiation in populations. In this paper we provide a comprehensive set of estimators of the most common statistics in population genetics based on the frequency spectrum, namely the Watterson estimator <em style="background-color: transparent; border: 0px; font-size: 12px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">θ</em><sub style="background-color: transparent; border: 0px; font-size: 0.8em; line-height: 0.7em; margin: 0px; outline: 0px; padding: 0px; white-space: nowrap;"><em style="background-color: transparent; border: 0px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">W</em></sub>, nucleotide pairwise diversity II, Tajima's D, Fu and Li's D and F, Fay and Wu's <em style="background-color: transparent; border: 0px; font-size: 12px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">H</em>, McDonald-Kreitman and HKA tests and <em style="background-color: transparent; border: 0px; font-size: 12px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Fst</em>, corrected for sequencing errors and ascertainment bias. In a simulation study, we show that pool and individual <em style="background-color: transparent; border: 0px; font-size: 12px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">θ</em> estimates are highly correlated and discuss how the performance of the statistics vary with read depth and sample size in different evolutionary scenarios. As an application, we reanalyze sequences from <em style="background-color: transparent; border: 0px; font-size: 12px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Drosophila mauritiana</em> and from an evolution experiment in <em style="background-color: transparent; border: 0px; font-size: 12px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Drosophila melanogaster</em>. These methods are useful for population genetic projects with limited budget, study of communities of individuals that are hard to isolate, or autopolyploid species.</div>
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<a href="http://onlinelibrary.wiley.com/doi/10.1111/mec.12522/abstract">http://onlinelibrary.wiley.com/doi/10.1111/mec.12522/abstract</a></div>
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Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-8849033840157549772013-09-16T17:19:00.002-07:002013-09-16T17:19:37.666-07:00mdesci1. <a href="http://www.medsci.cn/">http://www.medsci.cn/</a><br />
<br />
2. <span style="background-color: #e4f0fa; color: #205d99; font-family: 'Trebuchet MS', Verdana, Arial, Helvetica, sans-serif; font-size: 14px; font-weight: bold; letter-spacing: 2px; text-align: center;">2013自然科学基金查询与分析系统(基础查询版)</span><br />
<a href="http://www.medsci.cn/sci/nsfc.do">http://www.medsci.cn/sci/nsfc.do</a><br />
<br />
3. <span style="background-color: #e4f0fa; color: #205d99; font-family: 'Trebuchet MS', Verdana, Arial, Helvetica, sans-serif; font-size: 12px; font-weight: bold; letter-spacing: 2px; text-align: center;">MedSci 2013年期刊智能查询系统(2012年度)</span><br />
<a href="http://www.medsci.cn/sci/submit.asp">http://www.medsci.cn/sci/submit.asp</a><br />
<br />
4. 论文服务<br />
<a href="http://www.medsci.cn/list.asp?classid=110">http://www.medsci.cn/list.asp?classid=110</a><br />
<br />Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-39608417099143684832013-09-16T17:10:00.002-07:002013-09-16T17:10:53.198-07:00public library of bioinformatics1. <a href="http://www.plob.org/">http://www.plob.org/</a><br />
public library of bioinformatics<br />
<br />
2. <a href="http://www.bioask.net/">http://www.bioask.net/</a>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-18455619715066184042013-09-14T23:38:00.004-07:002013-09-14T23:38:49.810-07:00forest plot<a href="https://mcfromnz.wordpress.com/2012/11/06/forest-plots-in-r-ggplot-with-side-table/#more-356">https://mcfromnz.wordpress.com/2012/11/06/forest-plots-in-r-ggplot-with-side-table/#more-356</a><br />
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<div class="separator" style="clear: both; text-align: center;">
<a href="http://mcfromnz.files.wordpress.com/2012/11/forest_plot_1.png?w=584" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="160" src="http://mcfromnz.files.wordpress.com/2012/11/forest_plot_1.png?w=584" width="320" /></a></div>
<br />Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-28525405625239197732013-09-14T23:15:00.001-07:002013-09-14T23:15:26.489-07:00BroadE Workshop 2013 July 9-10<a href="http://www.broadinstitute.org/gatk/guide/events?id=3093#materials">http://www.broadinstitute.org/gatk/guide/events?id=3093#materials</a><br />
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<span style="background-color: white; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px;">This workshop covered the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. View the </span><a href="http://www.broadinstitute.org/gatk/guide/events?id=3093#materials" style="background-color: white; color: #269abc; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px; text-decoration: none;">workshop materials</a><span style="background-color: white; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px;"> to learn why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.</span><br />
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Workshop materials</h3>
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<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-A01-Opening_Day1.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Day 1 - Opening remarks</h4>
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<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-0A-Intro_to_NGS.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5175" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Introduction to Next Generation Sequence Analysis</h4>
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<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-0B-Intro_to_GATK.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5176" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Introduction to the GATK</h4>
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<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-1-Map_and_Dedup.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5177" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Mapping and duplicate marking (data pre-processing)</h4>
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<div class="well" style="-webkit-box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; background-color: whitesmoke; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; border: 1px solid rgba(0, 0, 0, 0.0470588); box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px; margin-bottom: 20px; min-height: 20px; padding: 19px;">
<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-2-Realignment.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5178" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Local realignment around indels<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">RTC</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">IR</span></div>
</h4>
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<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-3-Base_recalibration.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5179" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Base quality score recalibration (BQSR)<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">BR</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">PR</span></div>
</h4>
</div>
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<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-4-Compression.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5180" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Compression with ReduceReads<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">RR</span></div>
</h4>
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<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-A02-Opening_Day2.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Day 2 - Opening remarks</h4>
</div>
<div class="well" style="-webkit-box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; background-color: whitesmoke; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; border: 1px solid rgba(0, 0, 0, 0.0470588); box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px; margin-bottom: 20px; min-height: 20px; padding: 19px;">
<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-5-Variant_calling.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5181" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Variant calling<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">UG</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">HC</span></div>
</h4>
</div>
<div class="well" style="-webkit-box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; background-color: whitesmoke; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; border: 1px solid rgba(0, 0, 0, 0.0470588); box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px; margin-bottom: 20px; min-height: 20px; padding: 19px;">
<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-6-Variant_recalibration.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5182" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Variant quality score recalibration (VQSR)<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">VR</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">AR</span></div>
</h4>
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<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-7A-Genotype_refinement.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5183" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Genotype phasing and refinement<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">PBT</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">RBP</span></div>
</h4>
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<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-7B-Functional_annotation.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5184" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Functional annotation<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">VA</span></div>
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<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-8-Variant_analysis.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/node/5185" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Analyzing variant calls<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">SV</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">CV</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">VE</span></div>
</h4>
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<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-BP-9-Parallelism.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - Introduction to Parallelism (video not available yet)<div class="pull-right" style="float: right;">
<span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">NT</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">NCT</span> <span class="badge badge-info" style="background-color: #3a87ad; border-bottom-left-radius: 9px; border-bottom-right-radius: 9px; border-top-left-radius: 9px; border-top-right-radius: 9px; color: white; font-size: 10.998px; line-height: 14px; padding: 1px 9px 2px; text-shadow: rgba(0, 0, 0, 0.247059) 0px -1px 0px; vertical-align: baseline; white-space: nowrap;">Q</span></div>
</h4>
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<h3 style="background-color: white; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 18px; line-height: 27px; margin: 0px; text-rendering: optimizelegibility;">
Supplemental materials</h3>
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<div class="well" style="-webkit-box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; background-color: whitesmoke; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; border: 1px solid rgba(0, 0, 0, 0.0470588); box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px; margin-bottom: 20px; min-height: 20px; padding: 19px;">
<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/GATKwh1-Z1-GenomeSTRiP.pdf" style="color: #269abc; text-decoration: none;"><span class="icon-desktop" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - <a href="http://www.broadinstitute.org/gatk/events/3093/http://www.broadinstitute.org/node/5186" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - GenomeSTRiP: Discovery and genotyping of deletions</h4>
</div>
<div class="well" style="-webkit-box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; background-color: whitesmoke; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; border: 1px solid rgba(0, 0, 0, 0.0470588); box-shadow: rgba(0, 0, 0, 0.0470588) 0px 1px 1px inset; color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px; line-height: 18px; margin-bottom: 20px; min-height: 20px; padding: 19px;">
<h4 style="color: inherit; font-family: inherit; font-size: 14px; margin: 0px; text-rendering: optimizelegibility;">
<a href="http://www.broadinstitute.org/gatk/events/3093/http://www.broadinstitute.org/node/5187" style="color: #269abc; text-decoration: none;"><span class="icon-film" style="-webkit-font-smoothing: antialiased; background-image: none; background-position: 0% 0%; background-repeat: repeat repeat; display: inline; font-family: FontAwesome; font-weight: normal; height: auto; line-height: normal; margin-top: 0px; text-decoration: inherit; vertical-align: baseline; width: auto;"></span></a> - XHMM: Discovery and genotyping of copy number variation from exome read depth (PDF not available for download yet)</h4>
</div>
Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-54661218696098934552013-09-09T22:06:00.003-07:002013-09-09T22:06:57.146-07:002013年龙星计划之生物信息学<a href="http://yixf.name/2013/09/04/%E8%8D%902013%E5%B9%B4%E9%BE%99%E6%98%9F%E8%AE%A1%E5%88%92%E4%B9%8B%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E5%AD%A6/">http://yixf.name/2013/09/04/%E8%8D%902013%E5%B9%B4%E9%BE%99%E6%98%9F%E8%AE%A1%E5%88%92%E4%B9%8B%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E5%AD%A6/</a><br />
<br />
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课程主页</h3>
<div style="background-color: white; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 14px; line-height: 24px; margin-bottom: 0.75em; padding: 0px;">
<a href="http://admis.fudan.edu.cn/ds2013/" style="color: #0063dc; outline: none; text-decoration: none;">2013龙星计划课程复旦生物信息</a></div>
<h3 style="background-color: white; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 15px; line-height: 24px; margin: 0px 0px 0.75em; padding: 0px;">
课件下载</h3>
<div style="background-color: white; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 14px; line-height: 24px; margin-bottom: 0.75em; padding: 0px;">
<a href="http://admis.fudan.edu.cn/ds2013/" style="color: #0063dc; outline: none; text-decoration: none;">理论课幻灯片与实验课材料</a></div>
<h3 style="background-color: white; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 15px; line-height: 24px; margin: 0px 0px 0.75em; padding: 0px;">
课程视频</h3>
<div style="background-color: white; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 14px; line-height: 24px; margin-bottom: 0.75em; padding: 0px;">
<a href="http://www.youku.com/playlist_show/id_19532648.html" style="color: #0063dc; outline: none; text-decoration: none;">2013龙星计划课程复旦生物信息(优酷网)</a></div>
<h3 style="background-color: white; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 15px; line-height: 24px; margin: 0px 0px 0.75em; padding: 0px;">
课程简介</h3>
<ul style="background-color: white; background-repeat: no-repeat repeat; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 14px; line-height: 24px; margin: 0px 0px 0px 35px; padding: 0px;">
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 1. Background. Basic Statistics. Introduce deep sequencing data. Motivational examples.</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 2. Analyze RNA-seq data and small RNA-seq data.</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 3. DNA methylation, Integration with other data types.</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 4. Analyze ChIP-seq data on transcription factors and histone modifications. Integration with other sequencing data types.</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 5. Analyze DNase-seq data and MNase-seq data. Integration with other data types.</div>
</li>
</ul>
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实验内容</h3>
<ul style="background-color: white; background-repeat: no-repeat repeat; color: #333333; font-family: 'Lucida Grande', Geneva, Arial, Verdana, 'Lucida Sans Unicode', Helvetica, sans-serif; font-size: 14px; line-height: 24px; margin: 0px 0px 0px 35px; padding: 0px;">
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 1. Background. Basic Statistics. Introduce deep sequencing data. Motivational examples.</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 2. Analyze ChIP-seq data on transcription factors and histone modifications. Integration with other sequencing data types.</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 3. Analyze RNA-seq data and small RNA-seq data</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 4. Analyze DNase-seq data and MNase-seq data. Integration with other data types</div>
</li>
<li style="margin: 0px; padding: 0px;"><div style="margin-bottom: 0.75em; padding: 0px;">
Day 5. DNA methylation, Integration with other data types</div>
</li>
</ul>
Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-16565952703660719672013-09-09T22:02:00.003-07:002013-09-09T22:02:58.300-07:00MOSAIK: A hash-based algorithm for accurate next-generation sequencing read mapping<a href="http://arxiv.org/pdf/1309.1149v1.pdf">http://arxiv.org/pdf/1309.1149v1.pdf</a><br />
<br />
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation<br />
sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align<br />
reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD,<br />
Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to<br />
provide consistent mappings for all the generated data (sequencing technologies, low-coverage and<br />
exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash<br />
clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture<br />
mismatches as well as short insertions and deletions. To support the growing interest in larger structural<br />
variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g.<br />
mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All<br />
variant discovery benefits from an accurate description of the read placement confidence. To this end,<br />
MOSAIK uses a neural-net based training scheme to provide well-calibrated mapping quality scores,<br />
demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities<br />
greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is<br />
provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is<br />
multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO<br />
(http://gkno.me).Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-50770256251660766312013-08-23T16:34:00.000-07:002013-08-23T16:34:05.032-07:00一个新生境下物种形成的实例Rapid speciation with gene flow following the formation of Mount Etna<br />
<br />
<a href="http://gbe.oxfordjournals.org/content/early/2013/08/23/gbe.evt127.full.pdf+html">http://gbe.oxfordjournals.org/content/early/2013/08/23/gbe.evt127.full.pdf+html</a><br />
<br />
<span style="background-color: white; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px;">Environmental or geological changes can create new niches which drive ecological species divergence without the immediate cessation of gene flow. However, few such cases have been characterised. On the recently formed volcano, Mt. Etna, </span><em style="background-color: white; border: 0px; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px; margin: 0px; outline-style: none; padding: 0px; vertical-align: baseline;">Senecio aethnensis</em><span style="background-color: white; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px;"> and </span><em style="background-color: white; border: 0px; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px; margin: 0px; outline-style: none; padding: 0px; vertical-align: baseline;">S. chrysanthemifolius</em><span style="background-color: white; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px;"> inhabit contrasting environments of high and low altitude respectively. They have very distinct phenotypes, despite hybridising promiscuously, and thus may represent an important example of ecological speciation ‘in action’, possibly as a response to the rapid geological changes which Mt. Etna has recently undergone. To elucidate the species' evolutionary history, and help establish the species as study system for speciation genomics, we sequenced the transcriptomes of the two Etnean species, and the outgroup, </span><em style="background-color: white; border: 0px; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px; margin: 0px; outline-style: none; padding: 0px; vertical-align: baseline;">S. vernalis</em><span style="background-color: white; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px;">, using Illumina sequencing. Despite the species' substantial phenotypic divergence, synonymous divergence between the high- and low-altitude species was low (d</span><em style="background-color: white; border: 0px; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px; margin: 0px; outline-style: none; padding: 0px; vertical-align: baseline;">S</em><span style="background-color: white; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px;"> = 0.016 ± 0.017 [SD]). A comparison of species divergence models with and without gene flow provided unequivocal support in favor of the former and demonstrated a recent time of species divergence (153,080 ya ± 11,470[SE]) that coincides with the growth of Mount Etna to the altitudes which separate the species today. Analysis of d</span><em style="background-color: white; border: 0px; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px; margin: 0px; outline-style: none; padding: 0px; vertical-align: baseline;">N</em><span style="background-color: white; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px;">/d</span><em style="background-color: white; border: 0px; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px; margin: 0px; outline-style: none; padding: 0px; vertical-align: baseline;">S</em><span style="background-color: white; font-family: 'Lucida Grande', 'Lucida Sans Unicode', Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 13.63636302947998px; line-height: 19.09090805053711px;">revealed wide variation in selective constraint between genes, and evidence that highly expressed genes, more ‘multifunctional’ genes and those with more paralogues were under elevated purifying selection. Taken together, these results are consistent with a model of ecological speciation, potentially as a response to the emergence of a new, high altitude niche as the volcano grew.</span>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-1743030085077771182013-08-18T11:30:00.000-07:002013-08-18T11:30:15.707-07:00Alternative forms for genomic clines<a href="http://onlinelibrary.wiley.com/doi/10.1002/ece3.609/full">http://onlinelibrary.wiley.com/doi/10.1002/ece3.609/full</a><br />
<br />
<span style="background-color: #e9eff0; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px;">Understanding factors regulating hybrid fitness and gene exchange is a major research challenge for evolutionary biology. Genomic cline analysis has been used to evaluate alternative patterns of introgression, but only two models have been used widely and the approach has generally lacked a hypothesis testing framework for distinguishing effects of selection and drift. I propose two alternative cline models, implement multivariate outlier detection to identify markers associated with hybrid fitness, and simulate hybrid zone dynamics to evaluate the signatures of different modes of selection. Analysis of simulated data shows that previous approaches are prone to false positives (multinomial regression) or relatively insensitive to outlier loci affected by selection (Barton's concordance). The new, theory-based logit-logistic cline model is generally best at detecting loci affecting hybrid fitness. Although some generalizations can be made about different modes of selection, there is no one-to-one correspondence between pattern and process. These new methods will enhance our ability to extract important information about the genetics of reproductive isolation and hybrid fitness. However, much remains to be done to relate statistical patterns to particular evolutionary processes. The methods described here are implemented in a freely available package “HIest” for the R statistical software (CRAN; </span><a href="http://cran.r-project.org/" shape="rect" style="background-color: #e9eff0; border: 0px; color: #007e8a; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title="Link to external resource: http://cran.r-project.org/">http://cran.r-project.org/</a><span style="background-color: #e9eff0; font-family: Arial, 'Lucida Grande', Geneva, Verdana, Helvetica, 'Lucida Sans Unicode', sans-serif; font-size: 12px; line-height: 18px;">).</span>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-1979385431504046882013-08-18T09:40:00.001-07:002013-08-18T16:06:14.020-07:00Theoretical Evolutionary Genetics - draft text1. <a href="http://evolution.genetics.washington.edu/pgbook/pgbook.html">http://evolution.genetics.washington.edu/pgbook/pgbook.html</a><br />
<br />
This would be a very good book on population genetics.<br />
<br />
<ul style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;">
<li><i>Theoretical Evolutionary Genetics</i> notes by Joseph Felsenstein of the University of Washington. Felsenstein kindly provides these free of charge at: <a href="http://evolution.genetics.washington.edu/pgbook/pgbook.html" style="color: #902090;">http://evolution.genetics.washington.edu/pgbook/pgbook.html</a></li>
</ul>
<span style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;">2. </span><i style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;">Evolution and Selection of Quantitative Traits</i><span style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;"> </span><span style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;">by Bruce Walsh and Michael Lynch. While this book is in draft form it is available from Bruce Walsh's web page at:</span><span style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;"> </span><a href="http://nitro.biosci.arizona.edu/zbook/NewVolume_2/newvol2.html" style="background-color: white; color: #902090; font-family: Georgia, serif; font-size: 15px;">http://nitro.biosci.arizona.edu/zbook/NewVolume_2/newvol2.html</a><span style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;"> </span><span style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;">(Bruce Walsh's web page is in general a fantastic source of information on all things population/quantitative genetics).</span><br />
<div>
<span style="background-color: white; color: #444444; font-family: Georgia, serif; font-size: 15px;"><br /></span></div>
<div>
<span style="color: #444444; font-family: Georgia, serif;"><span style="font-size: 15px;">3. from Withlock in UBC</span></span></div>
<div>
<a href="http://www.zoology.ubc.ca/~whitlock/bio434/">http://www.zoology.ubc.ca/~whitlock/bio434/</a><br />
<br />
4. <a href="http://www.iro.umontreal.ca/~hussinju/l2010/">http://www.iro.umontreal.ca/~hussinju/l2010/</a></div>
Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-90524018427881618342013-08-17T21:44:00.001-07:002013-08-18T11:00:09.613-07:00course materials of Population Genetics - a very good one <a href="http://darwin.eeb.uconn.edu/eeb348/">http://darwin.eeb.uconn.edu/eeb348/</a><br />
<br />
<br />Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-27217084548494584802013-08-14T22:22:00.001-07:002013-08-14T22:24:04.000-07:00gene coexpression network and Correlation networks1. <a href="http://www.rna-seqblog.com/data-analysis/expression-tools/canonical-correlation-analysis-cca-for-rna-seq-co-expression-networks/">http://www.rna-seqblog.com/data-analysis/expression-tools/canonical-correlation-analysis-cca-for-rna-seq-co-expression-networks/</a><br />
<br />
2. <a href="http://bioinformatics.oxfordjournals.org/content/29/6/717.full">http://bioinformatics.oxfordjournals.org/content/29/6/717.full</a><br />
<br />
3. <a href="http://www.yieldbooster.org/bioinformatic-tools">http://www.yieldbooster.org/bioinformatic-tools</a><br />
<br />
<br />Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-51769721829552151682013-08-14T22:17:00.002-07:002013-08-14T22:17:52.957-07:00tutorials for genomics, phylogenetics, and population genetics<a href="http://evomics.org/learning/all/">http://evomics.org/learning/all/</a><br />
<br />
<div style="background-color: white; border: 0px; color: #555555; font-family: Arial, sans-serif; font-size: 14px; line-height: 21px; margin-bottom: 1.2em; outline: 0px; padding: 0px; vertical-align: baseline;">
<span class="dropcap" style="background-color: transparent; background-position: initial initial; background-repeat: initial initial; border: 0px; float: left; font-size: 42px; font-weight: bold; line-height: 0.7em; margin: 5px 7px 0px 0px; outline: 0px; padding: 0px; position: relative; vertical-align: baseline;">T</span>his page lists all of the learning activities available on this site.</div>
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Workshop Tutorials</h3>
<div class="shortcode-unorderedlist arrow" style="background-color: white; border: 0px; color: #555555; font-family: Arial, sans-serif; font-size: 14px; line-height: 21px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
<div style="background-color: transparent; border: 0px; line-height: 1.5em; margin-bottom: 1.2em; outline: 0px; padding: 0px; vertical-align: baseline;">
</div>
<ul style="background-color: transparent; border: 0px; list-style: none; margin: 0px 0px 1.5em; outline: 0px; padding: 0px 0px 0px 30px; vertical-align: baseline;">
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/software-installation/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Software Installation">Software Installation</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/unix-tutorial/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="UNIX Tutorial">Unix Tutorial</a></li>
</ul>
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Genomics</h3>
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<ul style="background-color: transparent; border: 0px; list-style: none; margin: 0px 0px 1.5em; outline: 0px; padding: 0px 0px 0px 30px; vertical-align: baseline;">
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/assembly-and-alignment/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Assembly">Assembly</a></li>
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<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/assembly-and-alignment/abyss/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="ABySS">ABySS</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/assembly-and-alignment/bowtie/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Bowtie">Bowtie</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/assembly-and-alignment/metavelvet/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="metavelvet">Metavelvet</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/assembly-and-alignment/newbler/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Newbler">Newbler</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/assembly-and-alignment/stampy/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Stampy">Stampy</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/assembly-and-alignment/velvet/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Velvet">Velvet</a></li>
</ul>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/genomics/augustus/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="AUGUSTUS">AUGUSTUS</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/genomics/galaxy/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Galaxy">Galaxy</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/genomics/gbrowse/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="GBrowse">GBrowse</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/quality-assessment-and-control-of-sequence-data/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Quality Assessment and Control of Sequence Data">Quality Assessment and Quality Control of Sequence Data</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/genomics/scripture/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Scripture">Scripture</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/genomics/stacks/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Stacks">Stacks</a></li>
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Phylogenetics</h3>
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<ul style="background-color: transparent; border: 0px; list-style: none; margin: 0px 0px 1.5em; outline: 0px; padding: 0px 0px 0px 30px; vertical-align: baseline;">
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/beast/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="BEAST">Beast</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/datamonkey-and-hyphy/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Datamonkey and HyPhy">Datamonky and HyPhy</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/garli/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="GARLI">GARLI</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/gsi/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="GSI">GSI</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/jmodeltest/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="jModelTest">jModelTest</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/mrbayes/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="MrBayes">MrBayes</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/paml/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="PAML">PAML</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/paup/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="PAUP*">PAUP*</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/phylogenetics/phycas/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Phycas">Phycas</a></li>
</ul>
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<h3 style="background-color: white; border: 0px; color: #222222; font-family: 'Arial, sans-serif', sans-serif; font-size: 1.6em; font-weight: normal; line-height: 1.5em; margin: 0px 0px 0.5em; outline: 0px; padding: 0px; vertical-align: baseline;">
Population Genetics</h3>
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<ul style="background-color: transparent; border: 0px; list-style: none; margin: 0px 0px 1.5em; outline: 0px; padding: 0px 0px 0px 30px; vertical-align: baseline;">
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/population-genetics/lamarc/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Lamarc">LAMARC</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/population-genetics/structurama/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Structurama">Structurama</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/population-genetics/migrate-n/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Migrate-n">Migrate-n</a></li>
</ul>
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Programming</h3>
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<ul style="background-color: transparent; border: 0px; list-style: none; margin: 0px 0px 1.5em; outline: 0px; padding: 0px 0px 0px 30px; vertical-align: baseline;">
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/programming/perl/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Perl">Perl</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/programming/bioperl/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Bioperl">BioPerl</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/programming/biopython/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Biopython">Biopython</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/programming/bioconductor/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Bioconductor">Bioconductor</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/programming/introduction-to-r/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Introduction to R">Introduction to R</a></li>
</ul>
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</div>
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<h3 style="background-color: white; border: 0px; color: #222222; font-family: 'Arial, sans-serif', sans-serif; font-size: 1.6em; font-weight: normal; line-height: 1.5em; margin: 0px 0px 0.5em; outline: 0px; padding: 0px; vertical-align: baseline;">
Bioinformatics</h3>
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<ul style="background-color: transparent; border: 0px; list-style: none; margin: 0px 0px 1.5em; outline: 0px; padding: 0px 0px 0px 30px; vertical-align: baseline;">
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/bioinformatics/fastablast/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="FASTA/BLAST">FASTA/BLAST</a></li>
<li style="background-image: url(http://evomicsorg.wpengine.netdna-cdn.com/wp-content/themes/simplicity/functions/images/shortcode-arrow.png); background-position: 0% 0%; background-repeat: no-repeat no-repeat; border: 0px; list-style-type: none; margin: 0px; outline: 0px; padding: 0px 0px 0px 25px; vertical-align: baseline;"><a href="http://evomics.org/learning/bioinformatics/multiple-sequence-alignment/" style="background-color: transparent; border: 0px; color: #7fb335; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" title="Multiple Sequence Alignment">Multiple Sequence Alignment</a></li>
</ul>
</div>
Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-6830823649697141732013-08-12T17:06:00.002-07:002013-08-12T17:06:40.348-07:00perl tutorial<a href="http://web.guru99.com/perl-tutorials/">http://web.guru99.com/perl-tutorials/</a>Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0tag:blogger.com,1999:blog-60498355161433544.post-91854332261322122602013-08-12T16:10:00.001-07:002013-08-12T16:10:53.965-07:00hybrid zonehybrid zones allow us:<br />
(1) to quantify the genetic differences responsible for speciation,<br />
(2) to measure the diffusion of genes between diverging taxa,<br />
(3) to understand the spread of alternative adaptations.<br />
<br />Anonymoushttp://www.blogger.com/profile/06764820974461316133noreply@blogger.com0