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)

本数据集为核酸数据集。归档文件Nucleic-data.tar.gz包含两个一级目录，分别为真菌（Fungi）与变形菌门（Proteobacteria）。每个一级目录下均设有两个子目录：序列比对（Alignments）与系统发育树（Trees）。序列比对子目录中存放对应物种的小型核糖体亚基RNA（small ribosomal subunit RNA）比对序列，以及100组含15条序列的子比对序列，格式均为FASTA（fasta）。比对序列的名称采用UniProt（Uniprot）物种助记符。系统发育树子目录下设有五个子目录：PQ、MP、ML、ME与QP，各目录中均存放通过五种重建方法由比对序列生成的Newick格式系统发育树，树文件的名称与对应比对文件的名称完全一致。此外，该系统发育树子目录还包含用作参考的物种树，文件格式为Newick，同时配有PNG格式的图像文件。其中，真菌参考树图像中，子囊菌亚门（Pezizomycotina）的门、亚门及纲对应的分支均带有标注；变形菌门参考树图像中，对应纲级别的分支均带有标注。（归档文件总大小：456 KB）