1.2.5 NJDist Neighbor Joining Phylogeny from Distance Matrix J. Adachi & M. Hasegawa phylogeny njdist distances Distance Matrix File perl " $value" 3 phylip_dist perl 1 distopt NJDist Parameters UPGMA UPGMA (-u) perl ($value)? " -u":"" 1 branch Branch Length (-w) perl ($value)? " -w":"" 1 leastsq Least squares (-l) perl ($value)? " -l":"" 1 sequential sequential input form (PHYLIP) (-S) perl ($value)? " -S":"" 1 outgroup Branch number of Out group (-o) perl (defined $value)? " -o $value":"" 1 treefile Output Tree (.tre) file? (-T) perl ($value)? " -T $distances":"" 1 Topo_file Output Topology (.tpl) file? (-t) perl ($value)? " -t $distances":"" 1 tre_file *.tre perl $treefile tpl_file *.tpl perl $Topo_file eps_file *.eps perl $Topo_file || $treefile