 | MCALIGNAlignment of noncoding DNA sequences based on explicit models of indel evolution |
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MCALIGN Description
Reliable alignment of noncoding DNA is difficult due to the unknown pattern of insertion/deletion (indel) events. The number of nucleotide differences (shown in red) differs radically between the alternative alignments, but without other information it is impossible to say which is the more plausible. MCALIGN tackles this problem by aligning sequences using an explicit model of indel evolution, and finds the most probable alignment for a pair of sequences, or three sequences of know phylogenetic relationship. The indel evolution model has two parameters: (1) theta, the frequency indels relative to the frequency of nucleotide substitution; (2) w, a vector of relative frequencies of indels of different length. Models for some taxa are supplied, or a new model can be set up by the user. MCALIGN is a Monte Carlo-based program that is capable of aligning two or three sequences. Get MCALIGN and give it a try to fully assess its capabilities!
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