From Bioinformatics.Org Wiki
- ARB — Microbiologist's sequence database tool
- BioJava — The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
- Biopython — The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
- BioWish — Biowish is a C-extension for the Tcl/Tk scripting language
- BLAST — (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases
- clustalw — The famous ClustalW multiple alignment program
- clustalx — Clustal X provides a window-based user interface to the ClustalW multiple alignment program
- COTRASIF — a free tool for genome-wide detection of putative TFBS in the promoters of the eukaryotic genes.
- DNA-GUI — DNA Graphical User Interface
- EMBOSS — EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
- MPSRCH — MPSRCH™ is a suite of Smith-Waterman sequence analysis programs which run under Linux and Tru64 on Intel and Alpha.
- NCRNASCAN — a structural RNA genefinder
- PatScan — PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
- PKNOTS — RNA pseudoknot prediction
- Pratt — a pattern discovery tool
- readseq — Reads and writes nucleic/protein sequences in various format
- SEALS — SEALS (A System for Easy Analysis of Lots of Sequences) is a software package expressly designed for large-scale research projects in bioinformatics.
- sp2fasta — produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
- Toucan — A Java tool for regulatory sequence analysis: detecting over-represented motifs and modules in sets of co-regulated genes.
- tRNAscan-SE — tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
- WU-Blast — Washington U. BLAST
- UGENE — a free and open source DNA and protein sequence analysis tool. The goal of the project is to integrate most of the available command line utilities into a single graphical package.
- YASS — a genomic local alignment tool for processing nucleotides sequences