Software

Software

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Software Links

• Artemis: A DNA Sequence Viewer and Annotation Tool Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
  
• NCBI BLAST BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
  
• 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
  
• PubCrawler - An Update Alerting Service for PubMed and GenBank Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
  
• Genalysis Genome Analysis Toolkit Commercial tool for comparing whole genomes or large genetic sequences. Outputs lists of matches and dot-plots and supports web-based BLAST searches.
  
• Sight: Extendable parallel system for automatic genome analysis Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Has features for converting between naming systems, sequence retrieval, E-PCR, gene prediction, similarity search, protein pattern search, report formatting etc. Written in Java.
  
• The Sanger Centre: Software Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
  
• Software for Life Science Discovery geneticXchange provides powerful software for enterprise-level data integration and desktop biologists.
  
• AnnHyb - nucleotidic sequence manager Free software for working with and managing nucleotide sequences in multiple formats. Many features including sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.
  
• The FASTA package of sequence comparison programs William Pearson's package for fast sequence comparison
  
• Meta-MEME v2.0.1 Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
  
• Molecular Evolutionary Genetics Analysis (MEGA2) software Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
  
• Verbumculus Genetic Sequence Analyzer An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Executable for Sparc-Solaris, Sparc-Intel or Linux-Intel. Also available as a Java applet.
  
• Linux Software Encyclopedia - Bioinformatics Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
  
• DNA microarray software Guide to the selection of microarray software for use with cDNA microarrays. Includes reviews of DNA microarray software from many vendors. Commercial affiliations unknown.
  
• Biotechnix 3d All-in-one bioinformatics suite. Sequence analysis, annotation, internet integration, project management features. Includes 3D glasses for visualising structures. For Mac (including OS X).
  
• Computer Program for Polyphasic Taxonomy Analysis The proBiosys suite of programs compares phenetic, chemotaxonomic and nucleic acid sequence data. Algorithms for polyphasic taxonomy are available to construct Dendrograms, the suite is simple to use.
  
• XDigitize A visualization software system for evaluation of hybridisation experiments.
  
• PHRED - Base-Calling Software with Quality Information A widely-used program for calling DNA sequence bases from sequencer trace files.
  
• PREMIER Biosoft International Makers of Primer Premier PCR primer design software, Plasmid Premier plasmid vector map drawing software, and Array Designer cDNA microarray software.
  
• Phred/Phrap/Consed System Home Page basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
  
• www.COMPBIO.net Source code and research papers in computational biology. Includes downloadable Visualize molecule visualisation software which supports PDB and DAS files.
  
• AG BIODV Software Links to software developed by the AG BIODV group. Tools for consensus, alignment and definition. Both downloads and executables.
  
• WU-BLAST Archives WU-BLAST: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics."