Reference trees for three sets of organisms
The archive contains alignments of orthologous series of protein domains. In each alignment sequences are orthologs from different organisms. Names of sequences are Uniprot mnemonics of corresponding organisms. See tables in the file Organisms.xlsx for full names of the organisms. Names of files are Pfam AC's with figures (1, 2, ets.) added to distinguish different orthologous series from one Pfam family. In folders Metazoa25, Fungi45 and Proteobacteria45 there are alignments of full-size orthologous series, in other folders there are random selections of 10 and 15 (for Metazoa) or 15 and 30 (for Fungi and Proteobacteria) sequences from each orthologous series.
Tables of organisms
The file contains tables of organisms from which the protein domains were taken. There are three tables: with 25 Metazoa, 45 Fungi and 45 Proteobacteria. For each organism, its Uniprot mnemonic is presented, these mnemonics are used in alignments and trees. For Metazoa, taxonomic divisions are presented that allows to construct a binary (i.e. fully resolved) tree. For Fungi and Protebacteria also some taxonomic divisions are presented, just to simplify orientation in data.