Data from: MsaTM-DB: A large-scale empirical database linking alignment properties, substitution models, and gene-tree metrics in phylogenomics
Data files
Sep 03, 2026 version files 19.47 GB
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data.tar.gz
19.47 GB
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README.md
3.30 KB
Abstract
Phylogenomic inference requires empirical datasets that capture the diversity of molecular evolutionary processes, yet existing resources rarely provide standardized, per-locus alignment, model, and tree metrics. We present MsaTM-DB, a curated database comprising 965,545 loci from 420 eukaryotic phylogenomic studies, each annotated with 35 features spanning alignment properties, substitution parameters, and gene tree metrics. These data enable systematic investigation of heterogeneity in phylogenetic signal across diverse evolutionary contexts. An integrated pipeline and interactive R Shiny platform support distributional analyses, correlation exploration, and empirically informed simulations. Using this database, we illustrate its downstream potential through exploratory analyses showing that alignment- and tree-derived features can help evaluate factors influencing phylogenetic support. MSA-TM-DB provides an extensive empirical foundation for benchmarking phylogenetic methods, guiding marker selection, and developing data-driven evolutionary models. Our database is available online at https://github.com/xtmtd/MSA-and-tree-metrics-exploration
Dataset DOI: 10.5061/dryad.j3tx95xw7
Description of the data and file structure
README
MsaTM‑DB Raw Data Archive
This repository contains the raw phylogenomic datasets used in the manuscript:
“MsaTM‑DB: a large‑scale empirical database linking alignment properties, substitution models, and gene‑tree metrics in phylogenomics.”
The archived data include all original multiple sequence alignments (MSAs), gene trees, and reference trees used to construct the MsaTM‑DB feature tables.
1. Directory Structure
The top-level directory contains a folder named data/, which organizes all raw datasets into four major biological groups:
- Animals — folder name starts with A
- Fungi — folder name starts with F
- Other Eukaryotes — folder name starts with O
- Plants — folder name starts with P
Example directory layout:
data/
│
├── Animals/ (A000001 – A000349, except A000234)
├── Fungi/
├── Other/
└── Plants/
Note on missing dataset A000234
Dataset A000234 was excluded because the original published data were incomplete or of insufficient quality.
As a result, the numbering in the Animals group skips from A000233 directly to A000235, and A000234 is not included and was not used in any downstream analyses.
2. Contents of Each Dataset Folder
Each dataset folder (e.g., P000151/) contains:
P000151/
│── gene_trees/ (per‑locus inferred gene trees)
│── MSAs/ (per‑locus sequence alignments)
└── ref.tre (reference species tree)
MSAs
Stored in the MSAs/ directory, named as:
P000151_L001.fas
...
P000151_L226.fas
Gene Trees
Stored in gene_trees/, named as:
P000151_L001.tre
...
P000151_L226.tre
Reference Tree
ref.tre
3. File Examples
Example files provided:
- P000151_L001.fas — sample alignment
- P000151_L001.tre — sample gene tree
- ref.tre — sample reference tree
4. Usage Notes
- Taxon names are standardized across all MSAs, gene trees, and reference trees.
- Locus indices (L001–Lxxx) correspond exactly between MSAs and gene trees.
- Data here are raw inputs used to generate the 35 MsaTM‑DB features.
5. Citation
Please cite the manuscript:
Zhan, Z.-H. & Zhang, F. 2026. MsaTM-DB: a large-scale empirical database linking alignment properties, substitution models, and gene-tree metrics in phylogenomics. Palaeoentomology, 9(4): 374–382. https://doi.org/10.11646/palaeoentomology.9.4.9
Files and variables
File: data.tar.gz
Description: data used for this study
Access information
Other publicly accessible locations of the data:
Data was derived from the following sources: