DOI: 10.5061/dryad.18931zd64
title: Data from: AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test

description: The core of molecular phylogeny is the inference of a tree diagram
 representing the evolutionary relatedness among nucleotide or amino acid
 sequences. In addition, evaluating the credibility of “bipartitions,” each
 of which splits the inferred tree into two subtrees, is an indispensable
 part of modern phylogenetic studies. The most popular method for examining
 the credibility of bipartitions in a phylogenetic tree is the bootstrap.
 In the maximum likelihood framework, two alternative methods for the
 bootstrap, UFBoot2 and SH-aLRT, are available. In this study, we propose a
 new software “AUTOEB,” which evaluates bipartitions in a given
 phylogenetic tree employing an approximately unbiased (AU) test. For each
 bipartition, the software generates two alternative trees from a given
 tree by disrupting the bipartition of interest with the minimum changes in
 tree topology and compares them by the AU test. In the case of either or
 both alternative trees failing to be rejected, the software calls the
 particular bipartition “unresolved” and otherwise “resolved.” We
 phylogenetically analyzed four empirical sequence data and demonstrated
 that AUTOEB can provide an alternative criterion toward bipartitions that
 received high support values from the pre-existed methods, and help to
 evade potential false interpretations based on phylogenetic trees.
description: We prepared three multiprotein alignments, as well as a
 single-gene (16S rDNA) alignment. The first multiprotein alignment,
 “euk340,” comprises 340 proteins (116,499 amino acid positions in total)
 sampled from 97 phylogenetically diverse eukaryotes. This alignment is
 identical to that analyzed in Harada et al. (Mol Biol Evol 2024
 41:msae014).<br>We here prepared two new multiprotein alignments
 designated “arc50” and “bac104.” The proteins contained in arc50 were
 chosen from 53 phylogenetically informative markers (arc53) in the Genome
 Taxonomy Database Release 214 (GTDB R214). Among the genomes available for
 each order in Archaea, a single genome with the greatest completeness was
 retained, remaining 149 genomes for the alignment. Then, three proteins,
 which are absent in more than 79 out of the 149 genomes, were omitted.
 single-protein alignments were prepared by MAFFT (version: 7.505) under
 the L-INS-i model, followed by trimming of ambiguously aligned positions
 and those with high gap propositions by BMGE (version: 2.0) with -g 0.2 -e
 0.3 option. The final multiprotein alignment was generated by
 concatenating the 50 single-protein alignments sampled from the 149
 archaeal species (12,425 amino acid positions in total). The procedure
 described above was repeated to prepare bac104. 490 genomes with high
 completeness, each representing an order in Bacteria, were selected for
 multiprotein phylogenetic analyses. Among the 120 phylogenetically
 informative markers (bac120) in the GTDB R214, we omitted 16 proteins that
 are absent in more than 190 out of the 490 genomes. The final multiprotein
 alignment was generated by concatenating the 104 single-protein alignments
 sampled from 490 bacterial species (28,182 amino acid positions in
 total). We obtained the nucleotide sequences of small
 subunits of ribosomal RNA gene (16S rDNA) of the species in Bacteria and
 Archaea from the GTDB as of July 26, 2023. First, we selected 3,823
 genomes, each of which is classified as representatives and with the
 greatest completeness among those sampled from each family in
 Archaea/Bacteria. Then, the 16S rDNA sequences were retrieved from the
 selected genomes. The 16S rDNA sequences were aligned by MAFFT (version:
 7.505) under the L-INS-i model. Ambiguously aligned positions and the
 positions with high gap proportions in the alignment were discarded by
 trimAl (version: 1.4.rev15) with -gt 0.1 option. After the first alignment
 trimming, 784 sequences, in which gaps occupied more than 75% of the total
 positions, were removed from the initial alignment. We further discarded
 ambiguously aligned positions and the positions with high gap proportions
 by BMGE (version: 2.0) with -g 0.4 -e 0.3 option. Then, we subjected the
 alignment after the second trimming to preliminary phylogenetic analysis
 and removed 25 rapidly evolving (long branch) sequences that potentially
 bias the phylogenetic inferences. The final refinement of the alignment
 after the exclusion of the rapidly evolving sequences was done by BMGE
 with the same options. The final 16SrDNA alignment comprises 3,014
 sequences with 1,102 nucleotide positions. We used
 IQ-TREE (version: 2.2.0) for all the phylogenetic analyses conducted in
 this study. For the ML tree reconstruction from euk340 and arc50, the LG +
 C60 + F + G model, a site heterogeneous substitution model, was applied.
 The ML trees were inferred from bac104 under the LG + C20 + F + G model.
 The C20 option was set to account for the site heterogeneity in bac104, as
 the C60 option was too computationally intensive for this multiprotein
 alignment including 490 OTUs. The ML tree was inferred from 16SrDNA under
 the GTR + F + G model.
description: # Phylogenetic alignments and trees assessed in Bamba
 [https://doi.org/10.5061/dryad.18931zd64](https://doi.org/10.5061/dryad.18931zd64) ## Description of the data and file structure File name format: {dataset}_{size}.{file type} Dataset \- euk340: multiprotein MSA of Eukaryotes \- arc50: multiprotein MSA of Archaea \- bac104: multiprotein MSA of Bacteria \- 16SrDNA: single-gene MSA (16SrDNA) of Archaea and Bacteria Size \- full: Full sequence \- XX%: Sequence with randomly selected sites from "full" file File type \- XX.fasta: Multiple sequence alignment \- XX.treefile: ML tree reconstructed from XX.fasta ### Files and variables #### File: 16SrDNA\_full.treefile **Description:** The ML tree inferred from 16SrDNA_full.fasta #### File: 16SrDNA\_full.fasta **Description:** A phylogenetic alignment of 16SrDNA sequences from bacteria and archaea #### File: arc50\_25%.treefile **Description:** The ML tree inferred from a randomly selected 25% of the positions in arch50_full.fasta #### File: arc50\_25%.fasta **Description:** A phylogenetic alignment of randomly selected 25% of the positions in arch50_full.fasta #### File: arc50\_50%.treefile **Description:** The ML tree inferred from a randomly selected 50% of the positions in arch50_full.fasta #### File: arc50\_full.fasta **Description:** A phylogenetic alignment comprising 50 proteins conserved among archaea species #### File: arc50\_full.treefile **Description:** The ML tree inferred from arch50_full.fasta #### File: arc50\_50%.fasta **Description:** A phylogenetic alignment of randomly selected 50% of the positions in arch50_full.fasta #### File: euk340\_5%.treefile **Description:** The ML tree inferred from a randomly selected 5% of the positions in euk340_full.fasta #### File: bac104\_full.treefile **Description:** The ML tree inferred from bac104 alignment #### File: euk340\_20%.treefile **Description:** The ML tree inferred from a randomly selected 20% of the positions in euk340_full.fasta #### File: euk340\_20%.fasta **Description:** A phylogenetic alignment of randomly selected 20% of the positions in euk340_full.fasta #### File: euk340\_full.treefile **Description:** The ML tree inferred from arc50_full.fasta #### File: euk340\_full.fasta **Description:** A phylogenetic alignment comprising 340 proteins conserved among eukaryotes #### File: euk340\_5%.fasta **Description:** A phylogenetic alignment of randomly selected 5% of the positions in euk340_full.fasta (i.e., euk340 alignment) #### File: bac104\_full.fasta **Description:** A phylogenetic alignment comprising 104 proteins conserved among bacterial species