Software & Scripts - The Santos Lab

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Software & Scripts

The Santos Lab is happy to offer copies of various shell and perl scripts as well as software binaries related to biocomputing. Most of these should work on any UNIX/Linux operating system; however, some require a current version/installation of the Bioperl modules and/or are specific to Apple OSX with Intel hardware. Although some of these scripts have been written by members of the laboratory, most originate from the Stothard Research Group at the University of Alberta and the Advanced Center for Genome Technology at the University of Oklahoma. Another useful source for bioSoftware & Scripts is the "Tools" tab at the Natural Environment Research Council Environmental Bioinformatics Centre website.

To download a script, right-click on the link and select "Download linked file as...". Please read the comments in the scripts for additional information on their usage.

>> 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.

The Santos Lab also maintains an OpenSuse Build Service (OBS) repository of software packages for population genetics, phylogenetics, phylogenomics, bioinformatics and next-generation sequencing (NGS) "rolled" as RPMs for CentOS 6 (these also work with Scientific Linux 6 [which we prefer] and other RHEL 6 clones). Consult the documentation of your particular EL6 Linux distribution for instructions on how to add additional software repositories to your system.

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