Berkeley Phylogenomics Group

http://phylogenomics.berkeley.edu/ [open in a new window]

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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links directory index: 4963

Title	Publication Year	Google Scholar Citation Count
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis	2007	20
MUSCLE: multiple sequence alignment with high accuracy and high throughput	2004	4855
SATCHMO: sequence alignment and tree construction using hidden Markov models	2003	88
Phylogenetic inference in protein superfamilies: analysis of SH2 domains.	1998	0

NAR Web Server Issue 2007

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors