distmat calculates the evolutionary distances between every pair of sequences in a multiple alignment. The sequences must be aligned before running this program. Here is a sample session with distmat: % distmat pax.align Creates a distance matrix from multiple alignments Multiple substitution correction methods for proteins 0 : Uncorrected 1 : Jukes-Cantor 2 : Kimura Protein Method to use [0]: 2 Output file [outfile.distmat]: Mandatory qualifiers (bold if not always prompted): - [-msf] (seqset)
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File containing a sequence alignment. - -nucmethod (menu)
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Multiple substitution correction methods for nucleotides. - -protmethod (menu)
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Multiple substitution correction methods for proteins. - [-outf] (outfile)
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A name for the distance matrix. Optional qualifiers (bold if not always prompted): - -ambiguous (boolean)
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Use the ambiguous codes in the calculation of the Jukes-Cantor method, or if the sequences are proteins. - -gapweight (float)
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Weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods. - -position (integer)
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Choose base positions to analyse in each codon e.g., 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases. - -calculatea (boolean)
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Forces the calculation of the a-parameter in the Jin-Nei Gamma distance calculation. Otherwise, the default is 1.0 (see -parametera option). - -parametera (float)
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User-defined parameter to use in the Jin-Nei Gamma distance calculation. The suggested value (and default) is 1.0. |