Figure 8
From: RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
A phylogenetic tree for zinc-binding dehydrogenases produced by RIO This tree is based on the Pfam alignment adh_zinc (PF00107) and is a subtree of a larger tree. It has been calculated by the neighbor joining method using maximum likelihood pairwise distances [34] based on the BLOSUM 62 matrix [25]. Gene duplication are indicated by circles (inferred by our SDI algorithm [13]). The tree was rooted by minimizing the sum of duplications. The tree image was produced by ATV [33]. Species are represented by their SWISS-PROT abbreviations (ARATH: Arabidopsis thaliana, TOBAC: Nicotiana tabacum, MAIZE: Zea mays, MYCTU: Mycobacterium tuberculosis, BACSU: Bacillus subtilis, LEIMA: Leishmania major, HELPY: Helicobacter pylori, SYNY3: Synechocystis sp. strain PCC 6803, YEAST: Saccharomyces cerevisiae, KLULA: Kluyveromyces lactis, KLUMA: Kluyveromyces marxianus, CANAL: Candida albicans, EMENI: Emericella nidulans, SCHPO: Schizosaccharomyces pombe, CAEEL: Caenorhabditis elegans, BACST: Bacillus stearothermophilus). The A. thaliana query sequence F28P22_13 is labeled with Q. The bootstrap orthology values for potential orthologs are indicated in brackets. According to this tree, F28P22_13 has no orthologs.