Additional file 2 of PQ, a new program for phylogeny reconstruction

Protein data. The archive Protein-data.tar.gz contains nine folders that each hold data of one data set used in this work. Each folder contains two subfolders called Alignments and Trees. Subfolder Alignments contains sequence alignments in fasta format. Names of the files are Pfam identifiers with additional figures, for example, the file PF00012_3.fasta contains an alignment of the sequences of protein domains from the third orthologous group of Pfam family PF00012. Names of the sequences in alignments are Uniprot organism mnemonics. Subfolder Trees contains five subfolders, PQ, MP, ML, ME, and QP with trees in Newick format reconstructed from the alignments with five methods. Names of the tree files correspond to names of alignment files. The subfolder Trees of folders Metazoa-25, Fungi-45 and Proteobacteria-45 also contains the three species trees used as reference, in Newick format and as PNG images. On the metazoan tree image, all nontrivial branches are labeled with taxon names. On the fungal tree image, branches corresponding to phyla, subphyla, and classes of Pezizomycotina are labeled. On the proteobacterial tree image, branches corresponding to classes are labeled. (TAR 28,930 kb)