Additional file 3 of PQ, a new program for phylogeny reconstruction

Nucleic acid data. The archive Nucleic-data.tar.gz contains two folders called Fungi and Proteobacteria. Each folder contains two subfolders called Alignments and Trees. Subfolder Alignments contains the alignment of small ribosomal subunit RNA of corresponding organisms and 100 15-sequence subalignments in fasta format. 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. Also the subfolder Trees contains the species trees used as reference, in Newick format and as PNG images. 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 456 kb)