• Linux Software Encyclopedia - Bioinformatics
Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
• Meta-MEME v2.0.1
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the University of California-San Diego.
• Phred/Phrap/Consed System Home Page
basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
• PubCrawler: Update Alerting Service for PubMed/GenBank
Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
• The ARB Project
A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.
• GeneRunner for Windows
A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
• HMMER Profile Hidden Markov Models for Sequence Analysis
Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools
• Logical Depth
Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
• Molecular Evolutionary Genetics Analysis (MEGA2) software
Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
• PHRED: Base-Calling Software with Quality Information
A widely-used program for calling DNA sequence bases from sequencer trace files.
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