Multiple Sequence Alignments (MSAs) And Phylogenies

References

Textbooks

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
Felsenstein
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
Baldauf
Trends in Genetics 2003 19:345-351
PubMed

Models of molecular evolution and phylogeny.
Lio P and Goldman N
Genome Res 1998 8(12):1233-44
PubMed

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
PubMed

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

Primary Literature

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

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

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson J et al.
Nucleic Acid Res 1994 22(22):4673-80
PubMed

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson J et al.
Nucleic Acid Res 1997 25(24):4876-82
PubMed

MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
Edgar RC
BMC Bioinformatics 2004 5:113
PubMed

MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC
Nucleic Acid Res 2004 32(5):1792-7
PubMed

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K et al.
Nucleic Acid Res 2002 30(14):3059-66
PubMed

ProbCons: Probabilistic consistency-based multiple sequence alignment.
Do C et al.
Genome Res 2005 15(2):330-40
PubMed

An algorithm for progressive multiple alignment of sequences with insertions.
Loytynoja A and Goldman N
Proc Natl Acad Sci U S A 102(30):10557-62
PubMed

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Loytynoja A and Goldman N
Science 2008 320(5883):1632-5
PubMed

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

Back to Gibson Team course pages at EMBL.