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)

本数据集为蛋白质数据集。存档文件Protein-data.tar.gz内含九个文件夹，每个文件夹对应本研究使用的一组独立数据集。每个文件夹均包含两个名为Alignments与Trees的子文件夹。Alignments子文件夹内存储FASTA格式的序列比对文件，文件名采用带附加编号的蛋白质家族数据库（Pfam）标识符，例如文件PF00012_3.fasta包含Pfam家族PF00012的第三直系同源组的蛋白质结构域序列比对结果。比对文件中的序列名称采用通用蛋白质资源数据库（UniProt）的生物分类记忆码。Trees子文件夹内含五个子文件夹，分别为PQ、MP、ML、ME与QP，存储通过五种方法从序列比对结果重构得到的Newick（系统发育树标准格式）文件，树文件的文件名与对应比对文件的文件名完全一致。Metazoa-25、Fungi-45与Proteobacteria-45三个文件夹的Trees子文件夹，还额外包含三份作为参考的物种系统发育树，分别以Newick格式与便携式网络图形格式（PNG）图像形式存储。后生动物物种树图像中，所有非平凡分支均标注了分类单元名称；真菌物种树图像中，对应盘菌亚门（Pezizomycotina）的门、亚门与纲级分支均被标注；变形菌物种树图像中，对应纲级的分支均被标注。（存档大小：28930 KB）