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)

本数据集为蛋白质相关数据。归档文件Protein-data.tar.gz 包含九个文件夹，每个文件夹对应本研究中使用的一组数据集。每个文件夹下设两个子文件夹，分别为Alignments与Trees。Alignments子文件夹中存储FASTA格式的序列比对文件，文件名由Pfam标识符与附加标识组成。例如，文件PF00012_3.fasta 包含Pfam家族PF00012的第三直系同源组中蛋白质结构域的序列比对结果。比对文件内的序列名称采用UniProt生物体助记符。Trees子文件夹下设五个子文件夹，即PQ、MP、ML、ME与QP，存储通过五种不同重构方法从序列比对结果生成的Newick格式进化树文件。进化树文件的文件名与对应序列比对文件的文件名完全一致。Metazoa-25、Fungi-45以及Proteobacteria-45三个文件夹的Trees子文件夹中，还额外包含三份作为参考的物种进化树，分别为Newick格式文件与PNG格式图像文件。其中，后生动物进化树图像的所有非平凡分支均标注了分类单元名称；真菌进化树图像中，对应Pezizomycotina的门、亚门及纲级别的分支均被标注；变形菌门进化树图像中，对应纲级别的分支均被标注。（归档文件大小：28930 KB）