]> DISTMAT Creates a distance matrix from multiple alignments (EMBOSS) phylogeny:distance matrix http://bioweb.pasteur.fr/docs/EMBOSS/distmat.html distmat &emboss_init; input Input section sequence sequence -- gapany [set of sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 File containing a sequence alignment. gapany 8 seqsfile perl 1 advanced Advanced section nucmethod Method to use -- Multiple substitution correction methods for nucleotides (-nucmethod) 0 1 2 3 4 5 acd @(!$(acdprotein)) 0 perl " -nucmethod=$value" 2 Multiple substitution correction methods for nucleotides. protmethod Method to use -- Multiple substitution correction methods for proteins (-protmethod) 0 1 2 perl $acdprotein acd $acdprotein 0 perl " -protmethod=$value" 3 Multiple substitution correction methods for proteins. ambiguous Use the ambiguous codes in the calculation. (-ambiguous) 0 perl ($value)? " -ambiguous" : "" 4 Option to use the ambiguous codes in the calculation of the Jukes-Cantor method or if the sequences are proteins. gapweight Weight given to gaps (-gapweight) 0. perl (defined $value && $value != $vdef)? " -gapweight=$value" : "" 5 Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods. position Base position to analyse. (-position) 123 perl (defined $value && $value != $vdef)? " -position=$value" : "" 6 Choose base positions to analyse in each codon i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases. calculatea Calculate the a-parameter (-calculatea) 0 perl ($value)? " -calculatea" : "" 7 This will force the calculation of the a-parameter in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option). parametera a-parameter (-parametera) 1.0 perl (defined $value && $value != $vdef)? " -parametera=$value" : "" 8 User defined a parameter to be use in the Jin-Nei Gamma distance calculation. The suggested value to be used is 1.0 [Jin et al.] and this is the default. output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 9 auto perl " -auto -stdout" 10