Ncbi Entrez
NCBI recently started a biological image search feature (http://www.ncbi.nlm.nih.gov/images). This extension adds a figure summary in these figures. The summaries are derived from UWM's FigureSearch (http://figuresearch.askhermes.org). Note that the summary appears only for figures in open access...
Platforms: *nix
License: Freeware | Size: 71.68 KB | Download (33): figuresummarizer Download |
ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications. Besides using some RAM, ToBiX doesnt touch the host...
Platforms: *nix
License: Freeware | Size: 457.2 MB | Download (91): ToBiX Download |
Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (213): Bio::Tools::Run::TribeMCL Download |
DNALinux is a Linux distribution with bioinformatics software pre-installed. We believe that this distro fills an empty niche. Specialized biotech software usually is released as source code only and its not packaged for easy installation on "mainstream" Linux. Most scientific software is...
Platforms: *nix
License: Freeware | Size: 511 MB | Download (116): DNALinux Download |
BioBrew Linux is an open source Linux distribution that is enhanced for life scientists. It is customized for cluster and bioinformatics computing. It automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications....
Platforms: *nix
License: Freeware | Size: 1.93 GB | Download (120): BioBrew Linux Download |
Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (127): Bio::Tools::CodonTable Download |
Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling...
Platforms: *nix
License: Freeware | Size: 638 MB | Download (106): Vigyaan Download |
Bio::GMOD::Admin::Monitor::blat is a Perl module that can monitor a BLAT server. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $gmod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $gmod->live_version; Update a MOD installation...
Platforms: *nix
License: Freeware | Size: 71.68 KB | Download (106): Bio::GMOD::Admin::Monitor::blat Download |
Bio::GMOD is a unified API for Model Organism Databases. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $mod->live_version; Update a MOD installation use Bio::GMOD::Update;...
Platforms: *nix
License: Freeware | Size: 71.68 KB | Download (103): Bio::GMOD Download |
Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in...
Platforms: *nix
License: Freeware | Size: 2.3 MB | Download (122): Sequence Analysis Download |
Geneious Basic is your personalized library of genomic and genetic data; that provides a fully integrated, visually advanced toolset for:Sequence alignment and phylogeneticsSequence analysisBLAST, Protein structure viewing, NCBI, EMBL, Pubmed auto-find & moreAPI for creating your own plugins...
Platforms: Mac
License: Freeware | Download (91): Geneious Download |
FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra Features . Requirements: Python, Tandem...
Platforms: *nix
License: Freeware | Size: 20.48 KB | Download (48): FONZIE Download |
An automatically-updating library of genomic and genetic data; that provides a fully integrated, visually-advanced toolset for
- Sequence alignment and phylogenetics
- Sequence analysis, Contig assembly,
- primers, restriction analysis
- BLAST. Protein structure viewing, NCBI, UniProt, Pubmed...
Platforms: Mac
License: Freeware | Size: 77 MB | Download (58): Geneious for Mac OS Download |
WSciParser or Web Science Parser is a handy, small library developed in C#.NET specially designed to parse data from web science databases (ISI Web, NCBI, PubMed...)
for WindowsAll
Platforms: Windows
License: Freeware | Download (47): WSciParser Download |
CopyCat is a handy application specially designed to offer users an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies.
CopyCat offers various...
Platforms: Linux
License: Freeware | Size: 16 MB | Download (440): CopyCat for Linux Download |
CopyCat is a handy application specially designed to offer users an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies.
CopyCat offers various...
Platforms: Mac
License: Freeware | Size: 16 MB | Download (435): CopyCat for Mac OS X Download |
CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms. An overview of the CisPlusFinder can be found in the flowchart.tif file and is described in the following publication:
Pierstorff, N., C.M. Bergman &...
Platforms: Mac, BSD
License: Freeware | Size: 1.15 MB | Download (44): CisPlusFinder Download |
DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5
Platforms: Windows, Mac, Linux
License: Freeware | Size: 3.23 MB | Download (47): DNA Galaxy Download |
PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.PerlPrimer's current features include the following: - Calculation of...
Platforms: *nix, Perl, BSD
License: Freeware | Download (58): PerlPrimer Download |
BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and...
Platforms: Mac, Java 1.5 or later
License: Freeware | Size: 7.5 MB | Download (65): BlastViewer Download |