Download Mandatory qualifiers

[ Team LiB ]
distmat
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)
File containing a sequence alignment.
-nucmethod (menu)
Multiple substitution correction methods for nucleotides.
-protmethod (menu)
Multiple substitution correction methods for proteins.
[-outf] (outfile)
A name for the distance matrix.
Optional qualifiers (bold if not always prompted):
-ambiguous (boolean)
Use the ambiguous codes in the calculation of the Jukes-Cantor method, or if the sequences are
proteins.
-gapweight (float)
Weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods.
-position (integer)
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)