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EzTaxon : a web-based tool for identification of prokaryotes

The EzTaxon.org server contains a manually curated database of type strains of prokaryotes and provides identification tools using similarity based search. The algorithm behind the initial version can be found at Chun et al. (2007). The current version has advanced tools and up-to-date database for your identification jobs.

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PHYDIT : integrated software for rRNA sequence analysis

PHYDIT is a Microsoft Windows program for phylogenetic analysis of ribosomal RNA and protein sequence data.

jPHYDIT : integrated software for rRNA sequence analysis (JAVA version)

jPHYDIT stands for "Phylogenetic Editor for JAVA". jPHYDIT is an integrated graphical environment containing the following functions:

• Molecular sequence editor
• Semiautomated pairwsie alignment
• Manual editing of aligned sequences with RNA secondary structure information
• Various phylogenetic treeing algorithms
• Server-Client-based database management system (For MySQL)

CommCluster : a tool for comparing prokaryotic community structure

The study of microbial diversity and community analysis is very import in ecology field. CommCluster is a freely distributable implementation of comparing software for bacterial diversity and community structure.

MatchUp : a tool for primer/probe design

Matchup program can be used to find universal primers and group-specific probes for DNA-based detection methods llike AFLP(Amplification fragment length polymorphism) or Microarray experiment.