Multiple Sequence Alignments (MSAs) And Phylogenies



Molecular Systematics
Hillis et al.
Sinauer Associates, Inc., 1996, 978-0878932825
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Especially the chapter on Phylogenetic Inference by Swofford et al. pages 407-514

Fundamentals of Molecular Evolution
Graur and Li
Sinauer Associates, 2000, 978-0878932665
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General, easily-accessible introduction to the topic

Inferring Phylogenies
Sinauer Associates, 2003, 978-0878931774
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Very detailed descussion of the topic from one of the pioneers in the field. Goes into considerable mathematical details.

Review Articles

Molecular Phylogeny - Pitfalls and Progress
Moreira and Philippe
Intl Microbiol 2000 3:9-16

Phylogeny for the faint of heart: a tutorial
Trends in Genetics 2003 19:345-351

Troubleshooting Molecular Phylogenetic Analyses
Sanderson and Shaffer
Ann Rev Evol and Syst 2002 33:49-72

Multiple sequence alignment
Edgar and Batzoglou
Curr Opin Struct Biol 2006 16:368-73

Multiple sequence alignment
Pirovano and Heringa
Methods Mol Biol 2008 452:143-61

Selected Primary Literature

Evolutionary trees from DNA sequences: a maximum likelihood approach
Felsenstein J
J Mol Evol. 1981 17(6):368-76

Confidence-limits on phylogenies - an approach using the bootstrap
Felsenstein J
Evolution 1985 39(4):783-91

PDFs to many important molecular evolution articles (including some of these) can be found here

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