1.3 distquart - quartet inference by weak four-point method (NJ) Berry phylogeny distquart distquart seqlab distquart perl "distquart" 0 dist Reads as input inter-species distances (as opposed to sequences) (-d) perl ($value)? " -d1" : " -d0" 1 The program can take as input either a distance matrix (lower triangular) (infile.dist), either a character matrix in the file (infile.nuc) (ie, nucleotide sequences for the species in the same format as the PHYLIP package or as output by the readseq program) from which it computes the Hamming distance between species to infer the quartets. sequence_param Sequences parameters infile Nucleotide Sequences Alignement File perl "ln -s $infile infile.nuc; " -10 If you provide no distance matrix file, the Hamming distances will be computed from this file. 11 perl ! $dist readseq_ok_alig perl 1 gap Use gap position whenever is possible for computing the distance between two taxa (-g) perl ($value)? " -g1" : "" 0 1 If out, drop any position that contains a gap from the whole analysis. perl ! $dist correct Evolutionary model correction (-c) perl ($value)? " -c$value" : "" 0 1 0 0: no correction 1 1: correct according to the Jukes-Cantor 1969 model 2 2: correct according to the 2-param Kimura 1980 model perl ! $dist savedist Save in the file outfile.dist the inter-species Hamming distances computed from the input nucleotide sequences (-s) perl ($value)? " -s1" : "" 0 1 perl ! $dist distfile Distances matrix File (lower triangular) perl "ln -s $distfile infile.dist; " -10 perl $dist phylip_dist perl 1 lower Lower triangular distances matrix (-l) perl ($value)? " -l1" : "" 0 1 quartfile quartfile quartfile perl 1 outdistfile "outfile.dist" phylip_dist perl (! $dist) && $savedist