Difference between revisions of "Phylogenetic inference"

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Revision as of 21:43, 17 October 2013

Interpreting phylogenetic trees


This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.


Summary ...



 

Contents

   

Further reading and resources

Cocco et al. (2013) From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol 9:e1003176. (pmid: 23990764)

PubMed ] [ DOI ]

Li et al. (2013) Coevolution of quantum and classical strategies on evolving random networks. PLoS ONE 8:e68423. (pmid: 23874622)

PubMed ] [ DOI ]

Miyazawa (2013) Prediction of contact residue pairs based on co-substitution between sites in protein structures. PLoS ONE 8:e54252. (pmid: 23342110)

PubMed ] [ DOI ]

Burkoff et al. (2013) Predicting protein β-sheet contacts using a maximum entropy-based correlated mutation measure. Bioinformatics 29:580-7. (pmid: 23314126)

PubMed ] [ DOI ]

Ackerman et al. (2012) Accurate simulation and detection of coevolution signals in multiple sequence alignments. PLoS ONE 7:e47108. (pmid: 23091608)

PubMed ] [ DOI ]

Morcos et al. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U.S.A 108:E1293-301. (pmid: 22106262)

PubMed ] [ DOI ]

Clark et al. (2011) Using coevolution to predict protein-protein interactions. Methods Mol Biol 781:237-56. (pmid: 21877284)

PubMed ] [ DOI ]

Rodionov et al. (2011) A new, fast algorithm for detecting protein coevolution using maximum compatible cliques. Algorithms Mol Biol 6:17. (pmid: 21672226)

PubMed ] [ DOI ]

Kolesov & Mirny (2009) Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Biol 541:421-48. (pmid: 19381538)

PubMed ] [ DOI ]