1 Rapid reconstruction of phylogenies by the Neighbor-Joining method Kevin Howe, Alex Bateman, Richard Durbin Kevin Howe, Alex Bateman and Richard Durbin (2002). QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics 18(11):1546-1547. phylogeny quicktree quicktree perl ($distfile) ? "quicktree -in m" : "quicktree -in a" 0 distfile Distance matrix (-in m) perl " $value" 10 phylip_dist perl 1 You must enter either a distance matrix or a protein alignment perl ! $distfile && ! $aligfile Distance matrix and Protein alignment are mutually exclusive perl $distfile and $aligfile out Output (-out) perl (defined $value && $value ne $vdef) ? " -out $value" : "" t m distance matrix in Phylip format(m) t tree in New Hampshire format (t) 3 treeopt Tree output options upgma perl $out ne "m" Use the UPGMA method to construct the tree (-upgma) perl ($value) ? " -upgma" : "" 3 0 aligopt Alignment options aligfile Protein alignment file (instead of distance matrix) (-in a) perl ($value) ? " $value.stockholm" : "" 10 readseq_ok_alig perl 1 boot Calculate bootstrap values with n iterations (-boot) perl (defined $value) ? " -boot $value" : "" 3 Bootstrapping is not available for a matrix output perl $value && $out eq "m" Bootstrapping is not available for a matrix input perl $value && $distfile && (!$aligfile) kimura perl $aligfile ne "" Use the kimura translation for pairwise distances (-kimura) perl ($value) ? " -kimura" : "" 3 0 fastdnaml perl ($aligfile)? "readseq -p -f8 $aligfile > $aligfile.fasta ; sreformat stockholm $aligfile.fasta > $aligfile.stockholm; rm $aligfile.fasta ; " :"" -10 treefile perl $out ne "m" quicktree.out phylip_tree perl 1 distoutfile perl $out eq "m" quicktree.out phylip_dist perl 1 stockholmfile perl $aligfile "$aligfile.stockholm"