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HMMER - Profile hidden Markov models for biological sequence analysis.
Dynamite - Dynamite is a code generating language developed for sequence comparison methods.
- GENtle
- GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
- JAligner - Java implementation of biological sequence alignment algorithms
- JAligner is a Java implementation of biological sequence alignment algorithms. Presently, the package implements the pair wise alignment algorithm Smith-Waterman. The basic Dynamic Programming Smith-Waterman algorithm has been modified to support affine (open and extend) gap penalty. Also, Gotoh's improvement has been added to the algorithm to maintain the quadratic time complexity.
- E-CELL
- E-CELL Simulation Environment (E-CELL SE) is a software package for cellular and biochemical modeling and simulation.
- Wise2
- Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns.
- Jalview
- Jalview is a multiple alignment editor written entirely in java.
- VLinux
- VLinux is a Linux Live CD for Bioinformatics. It contains various sequence and structure analysis tools. The following packages are included in the present VLinux distribution. EMBOSS,GDE,Rasmol,PyMOL,GROMACS,Phylip,Arka/Genpak,ClustalW/ClustalX,TCoffee, Seaview,Garlic, Ramachandran Plot viewer, Primer, XMolCalc, NJPlot etc
- PhyloSort
- A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
- AnnHyb
- AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats. The features includes format conversion, sequence viewer, sequence editor, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination...
- DEODAS
- DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides
- Bioperl
- The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.
Genomorama - Genomorama is a software program for interactively displaying multiple genomes. It provides a powerful yet easy to use interface that leverages the visualization power of modern computers (via OpenGL) and the substantial bioinformatic infrastructure provided by the NCBI (via the NCBI C toolkit). Genomorama is written in portable, highly optimized C++ and comes in three "flavors" that allow it to run natively on (most) modern operating systems: OS X (using Carbon), Microsoft Windows (using MFC) and Linux (using Motif). Executables and source code are freely provided for all flavors.
- Pfam
- Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
- Geanfammer
- geanfammer contains divclus which divides proteinclusters into more correct domain level clusters
- ABE
- ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
- ALiBio: Algorithms Library for Bioinformatics
- The goal of ALiBio is the give libraries and efficient fundamental algorithm to be used when developing applications in the bioinformatics field.
- Genpak
- GP and Arka are lightweight programs for manipulation of DNA / RNA / protein sequences.
- Mavric
- Mavric is a python module for the manipulation and visualization of phylogenetic trees.
- autoseq
- autoseq is a small package of base calling software for ABI automated DNA sequencers. It is intended as a starting point for researchers interested in new base calling algorithms.
- SeqPup
- SeqPup is a biological sequence editor and analysis program.
gBioSeq - Biological sequence (ADN, protein) editor for GTK/Linux
- GeneX
- GeneX is not just an open source gene expression database. It also includes an XML specification for gene expression data exchange, as well as API to the database, XML format.
Readseq - Read & reformat biosequences
- DeltaStat
- DeltaStat performs statistical calculations on data from 2D gel experiments. DeltaStat combines the power of R, a language for statistics, with the efficiency of a relational database to handle the large amount of data generated in proteomics experiments.
- The Alkahest Initiative
- Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis. The goal is to produce a comprehensive package for data management and bioinformatics research which is composed of separable but interoperable modules which may be distributed among a number of computers. The software principly resides under Linux/UNIX, but its primary interface is a web application accessible through a browser on any platform.
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