PRANK (Probabilistic Alignment Kit) is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.
webPRANK is an easy-to-use web interface to the PRANK alignment algorithm.
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Phylogeny-aware alignment with PRANK.
Methods Mol Biol. 2014;1079:155-70. doi: 10.1007/978-1-62703-646-7_10.
BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N.
The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N.
Mol Biol Evol. 2012 Apr;29(4):1125-39. Epub 2011 Nov 1.