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Phylogenetic tree construction methods for estimating the evolutionary
histories of protein families provide powerful tools for the functional
annotation of unknown proteins
(Sjölander, "Phylogenomic inference of protein molecular function: advances and challenges," Bioinformatics 2004 (20)2:170-179.
Oxford University Press access
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PDF)
and in assisting
biologists in understanding the correlation between changes in protein
structure and function.
PhyloFacts includes phylogenetic tree construction for each protein family in
the resource.
After a multiple sequence alignment has been constructed for a protein family,
conservative masking protocols are applied to remove columns containing a large
number of gap characters.
We construct one or more phylogenetic trees for each PhyloFacts family:
neighbor-joining (from the PHYLIP suite), maximum parsimony (from PAUP),
and maximum likelihood (using the PHYML software).
We also construct a hierarchical tree and predict functional subfamilies using
the SCI-PHY (Subfamily Classification in PHYlogenomics) algorithm.
Details on how phylogenetic tree construction and analysis is employed in
PhyloFacts are available in
Krishnamurthy, Brown, Kirshner and Sjölander,
"PhyloFacts: An online structural phylogenomic encyclopedia for protein
functional and structural classification,"
Genome Biology 2006, 7:R83
The SCI-PHY subfamily identification method and experimental
validation on hundreds of protein families are available in
Brown, Krishnamurthy, and Sjölander,
"Automated Protein Subfamily Identification and Classification,"
PLoS Computational Biology 2007, 3(8): e160
doi:10.1371/journal.pcbi.0030160
(PDF).
SCI-PHY is also available as a stand-alone webserver at
http://phylogenomics.berkeley.edu/SCI-PHY.
The PhyloBuilder server provides clustering and alignment of homologs
followed by phylogenetic tree construction.
The server is described in
Glanville, Kirshner, Krishnamurthy and Sjölander,
"Berkeley Phylogenomics Group web servers: resources for structural
phylogenomic analysis,"
Nucleic Acids Research 2007; doi:10.1093/nar/gkm325
(PDF)
and is available at
http://phylogenomics.berkeley.edu/phylobuilder.
Another tree construction method developed by the Berkeley Phylogenomics
Group is SATCHMO (Simultaneous Alignment and Tree Construction using Hidden
Markov mOdels).
SATCHMO takes unaligned sequences and estimates a tree and alignment
simultaneously using hidden Markov models at each node in the tree.
Details and experimental validation are available at
Edgar and Sjölander, "SATCHMO: Sequence Alignment and Tree Construction using Hidden Markov models," Bioinformatics 2003 Jul 22;19(11):1404-11.
Oxford University Press access.
SATCHMO is also available as a stand-alone webserver at
http://phylogenomics.berkeley.edu/satchmo.
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