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)

核酸数据集。归档文件Nucleic-data.tar.gz包含两个子目录，分别为真菌（Fungi）与变形菌门（Proteobacteria）。每个子目录下均设有两个次级子目录：比对文件集（Alignments）与进化树文件集（Trees）。比对文件集次级子目录内存储了对应物种的小型核糖体亚基RNA序列比对结果，以及100组含15条序列的子比对文件，所有文件均采用fasta格式存储。比对序列的名称采用UniProt（Uniprot）物种助记符。进化树文件集次级子目录下设有五个次级子目录：PQ、MP、ML、ME与QP，每个目录内存储了通过五种不同算法基于序列比对结果重构得到的Newick格式进化树文件，进化树文件的文件名与对应比对文件的文件名完全一致。此外，进化树文件集次级子目录中还包含作为参考的物种进化树，这些文件同时提供Newick格式与PNG图像格式两种存储形式。真菌进化树的图像中，对应子囊菌亚门（Pezizomycotina）的门、亚门与纲级分类的分支均带有标注。变形菌门进化树的图像中，对应纲级分类的分支均带有标注。（归档文件大小：456 KB）