AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test

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..., 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).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 pr..., , # 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_f...