developmental network models - a new evolutionary model for phenotypic variation

http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01649.x/abstract

We develop an explicit genenetwork model with three components: some genes can receive environmental cues about the adult selective environment, some genesthat interact repeatedly to determine each others’ final state, and other factors that translate these final expression states into thephenotype. We show that the evolution of phenotypic plasticity is an important determinant of mutational patterns, genetic variance, andevolutionary potential of a population. Phenotypic plasticity tends to lead to populations with greater mutational variance, greater standinggenetic variance, and, when the optimal phenotypes of two traits vary in concert, greater mutational and genetic correlations. However,plastic populations do not tend to respond much more rapidly to selection than do populations evolved in a static environment. We find thatthe quantitative genetic descriptions of traits created by explicit developmental network models are evolutionarily labile, with genetic correlations that change rapidly with shifts in the selection regime.

a simulation work on deleterious mutations

Spatial heterogeneity in the strength of selection against deleterious alleles and the mutation load

tools for identifying repeat and transposons across the genomes

1. Identifying repeats and transposable elements insequenced genomes: how to find your way through the dense forest of programs

2. Transposon identification using profile HMMs

3. Repetitive Elements: Bioinformatic Identification, Classification and Analysis

4. Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes

tools for detecting tandem repeat across genomes

Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance

impede - 阻碍

Inability to obtain accurate heritability estimates under natural conditions has impeded studies of behavioural trait evolution.

evoke the question - 导致了问题

evoke, cause

This evokes the question: how many individuals and how many times does each individual need to be measured to obtain a precise estimate of repeatability.

reformat the reference items in Word accompanied by ENDnote

see this figure, after remove field code, the secret references' links were masked and you can freely reformat your references. This is for Mac users.

Following is the example for windows users.

A practical course on NGS analysis

EMBO Practical course: Bioinformatics and Comparative Genome Analyses

reference sheet for 4 interpreted languages

Interpreted Languages: PHP, Perl, Python, Ruby

SNP, indel calling from de novo assembly

1. fermi, https://github.com/lh3/fermi

2. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

alignment-free searching for conserved sequences across genomes

Long identical multispecies elements in plant and animal genomes

LIME

StatGen C++

StatGen C++, library and tools for handling and analyzing next generation sequencing and genotyping data

finding ultraconserved elements - an application of objective C

Multiple organism algorithm for finding ultraconserved elements

some courses on computational biology/genomics

http://bcc.bx.psu.edu/courses/

VAAST - the Variant Annotation, Analysis and Search Tool

VAAST (the Variant Annotation, Analysis and Search Tool) is a probabilistic search tool for identifying damaged genesand their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acidsubstitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unifiedlikelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and inan easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact ofboth types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can alsouse both rare and common variants to identify genes responsible for common diseases. VAAST thus has a muchgreater scope of use than any existing methodology.

Installing libsequence and analysis tools on OSX

Installing libsequence and analysis tools on OSX

VariScan

http://www.ub.edu/softevol/variscan/

population genetic tools for genome-scale data, including: VariScan, the PERL PopGen modules, and the libsequenceC++ library.

predict SNP effects using R

Assessing whether point mutations introduce stop codons into chromosomal DNA using Ensembland R

perlmodinstall2 - Installing Perl Modules

http://www.rcbowen.com/imho/perl/modules.html

concomitant increase - 伴随的增长

There was a concomitant increase in lifetime reproductive success as women whobegan their reproduction earlier generally had more children surviving toadulthood.