Berkeley Phylogenomics Group

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.

Topic

Phylogenomics;Sequence sites, features and motifs;Phylogenetics;Gene and protein families;Protein folds and structural domains

Detail

  • Operation: Tree-based sequence alignment;Multiple sequence alignment;Sequence alignment

  • Software interface: Web user interface

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  • Contact: kimmen@berkeley.edu

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Publications

  • SATCHMO: sequence alignment and tree construction using hidden Markov models.
  • Edgar RC and Sjölander K. SATCHMO: sequence alignment and tree construction using hidden Markov models. SATCHMO: sequence alignment and tree construction using hidden Markov models. 2003; 19:1404-11. doi: 10.1093/bioinformatics/btg158
  • https://doi.org/10.1093/bioinformatics/btg158
  • PMID: 12874053
  • PMC: -

Download and documentation

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