Auburn University   Biological Sciences

The Santos Lab

Homepage

Research

People

Publications

Journal Covers

Classes

Opportunities

Photo Gallery

 

Protocols

 

PCR Primers

 

Datasets

 

Search Databases

Symbiodinium Cultures

SD2-GED

SymBioSys

SYM Pub Search

 

Bookmarks

 

SYM DGGE Images

 

CNID-SYM Listserve

 

A-PONDS Listserve

 

Blogs

 

>>Software & Scripts

 

Login 2 Lab Server

 

Web Applications

SYM-BLAST

HALO-BLAST

EMBOSS

FaBox

WebLogo

PRIMACLADE

Primers4Clades

CODEHOP

CGView Server

In silico PCR

Calculate Oligo Tm

Microsat Finder

Get Protein Info

Basic Data Stats

IBDWS

MRBAYES WEB FORM

PAUP* WEB FORM

BIOMAIL

 
   

 

 

Software & Scripts

The Santos Lab maintains a GitHub repository as well as an OpenSuse Build Service (OBS) repository of scripts and software packages for population genetics, phylogenetics, phylogenomics, bioinformatics and next-generation sequencing (NGS). In the latter case, these are "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.

Examples from The Santos Lab on computational approaches and other CLI "tricks" are posted to Scott's Asciinema page, so also have a look to see what might be the latest there.

We also 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, many 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.

 
>> 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.
 

Back to faculty and staff