Phylogeny-aware alignment with PRANK (original) (raw)
Abstract
Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary and structural homology are not the same and sequence alignments generated with methods designed for structural matching can be seriously misleading in comparative and phylogenetic analyses. The phylogeny-aware alignment algorithm implemented in the program prank has been shown to produce good alignments for evolutionary inferences. Unlike other alignment programs, prank makes use of phylogenetic information to distinguish alignment gaps caused by insertions or deletions and, thereafter, handles the two types of events differently. As a by-product of the correct handling of insertions and deletions, prank can provide the inferred ancestral sequences as a part of the output and mark the alignment gaps differently depending on their origin in insertion or deletion events. As the algorithm infers the evolutionary history of the sequences, prank can be sensitive to errors in the guide phylogeny and violations on the underlying assumptions about the origin and patterns of gaps. These issues are discussed in detail and practical advice for the use of prank in evolutionary analysis is provided. The prank software and other methods discussed here can be found from the program home page at http://code.google.com/p/prank-msa/.
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References
- Sankoff D (1975) Minimal mutation trees of sequences. SIAM J Appl Math 28:35–42
Article Google Scholar - Ogurtsov A, Sunyaev S, Kondrashov A (2004) Indel-based evolutionary distance and mouse-human divergence. Genome Res 14:1610–1616
Article PubMed CAS Google Scholar - Hogeweg P, Hesper B (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol 20:175–186
Article PubMed CAS Google Scholar - Feng D, Doolittle R (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25:351–360
Article PubMed CAS Google Scholar - Löytynoja A, Goldman N (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320:1632–1635
Article PubMed Google Scholar - Löytynoja A, Goldman N (2005) An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci USA 102:10557–10562
Article PubMed Google Scholar - Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace I, Wilm A, Lopez R, Thompson J, Gibson T, Higgins D (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Article PubMed CAS Google Scholar - Edgar R (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Article PubMed CAS Google Scholar - Liu K, Raghavan S, Nelesen S, Linder C, Warnow T (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324:1561–1564
Article PubMed CAS Google Scholar - Fletcher W, Yang Z (2010) The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol 27:2257–2267
Article PubMed CAS Google Scholar - Jordan G, Goldman N (2012) The effects of alignment error and alignment filtering on the sitewise detection of positive selection. Mol Biol Evol 29:1125–1139
Article PubMed CAS Google Scholar - Dessimoz C, Gil M (2010) Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol 11:R37
Article PubMed Google Scholar - Landan G, Graur D (2007) Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol 24:1380–1383
Article PubMed CAS Google Scholar - Suchard M, Redelings B (2006) BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22:2047–2048
Article PubMed CAS Google Scholar - Novák A, Miklós I, Lyngsø R, Hein J (2008) StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics 24:2403–2404
Article PubMed Google Scholar - Löytynoja A, Vilella A, Goldman N (2012) Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28:1684–1691
Article PubMed Google Scholar - Löytynoja A, Goldman N (2010) webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11:579
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- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
Ari Löytynoja
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- Ari Löytynoja
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- Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
David J Russell
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Löytynoja, A. (2014). Phylogeny-aware alignment with PRANK. In: Russell, D. (eds) Multiple Sequence Alignment Methods. Methods in Molecular Biology, vol 1079. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-646-7\_10
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- DOI: https://doi.org/10.1007/978-1-62703-646-7\_10
- Published: 23 August 2013
- Publisher Name: Humana Press, Totowa, NJ
- Print ISBN: 978-1-62703-645-0
- Online ISBN: 978-1-62703-646-7
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