The Santos Lab

>> mapping_pe_reads_w_bwa_bowtie2.sh - Shell script for mapping Illumina reads to scaffold(s) in FASTA format. Needs working installation of BWA, SAMtools and Bowtie 2.

>> MPI-enabled MrBayes and PhyML - Precompiled binaries of the phylogenetic programs MrBayes and PhyML capable of utilizing multiple CPUs simultaneously (built for Apple Intel systems).

>> remote_blast_client.prl - Performs various BLAST searches against NCBI's databases.

>> blast_parse_all.prl - Parses BLAST reports for all HSPs with BioPerl's Bio::SearchIO module.

>> blast_parse_single.prl - Parses BLAST reports for single best HSP with BioPerl's Bio::SearchIO module.

>> blast2ps.prl - Creates a graphical representation of BLAST reports as a Postscript file.

>> blast2table.prl - Parses BLAST reports using BioPerl's Bio::Tools::Blast.pm; writes the data from each HSP in tabular form in a variety of formats.

>> bp_embl2picture.prl - Renders a GenBank or EMBL file into a PNG or GIF image.

>> compare_library.prl - Accepts two files (i and j) containing multiple DNA sequences in FASTA format and compares each sequence in file i to that in file j using a local BLAST installation.

>> count_types.sh - Counts how many files there are of each type in a directory.

>> NCBI_accession_retrieval.sh - Downloads sequences from NCBI in FASTA format when provided with a file containing accession numbers.

>> NCBI_condense_names.prl - Replaces entry names in downloaded FASTA sequences from NCBI with simplier names.

>> NCBI_retrieval.prl - Uses NCBI's Entrez Programming Utilities to perform interactive batch requests to NCBI Entrez.

>> split_fasta.prl - Accepts a file consisting of multiple FASTA formatted sequence records and splits them into multiple files.

>> nanorc.txt - Customized configuration file for use with the GNU Nano 2.0.7 text editor. Allows nucleotide highlighting in FASTA and NEXUS files. Save to your home directory as .nanorc and it will be sourced by Nano at start-up.