OrthoMaM processed mammalian multiple sequence alignments: Data from: Treeline provides a unified strategy for optimizing phylogenetic trees under alternative criteria
Data files
Jun 09, 2026 version files 217.67 MB
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omm_filtered_AA_CDS.tar
50.59 MB
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omm_filtered_NT_CDS.tar
167.08 MB
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README.md
1.34 KB
Abstract
OrthoMaM orthologous sequence alignments were used to test Treeline on a realistic application. Phylogenetic trees were generated for multiple optimization criteria using the complete alignments found here. Then, the branching order for a subset of five species belonging to the family Hominidae were compared to their commonly accepted species tree.
https://doi.org/10.5061/dryad.4qrfj6qms
Description of the data and file structure
Amino acid and nucleotide alignments were downloaded from OrthoMaM database version 12a for all genes with relative evolutionary rates greater than 1. Alignments were subset to the species present in the OrthoMaM species tree, sequences without ambiguities, and requiring the species Pan troglodytes, Pan paniscus, Homo sapiens, Gorilla gorilla, and Pongo abelii. Identical sequences were eliminated to ensure a bifurcating topology, resulting in 2,897 amino acid alignments with 9 to 156 (average = 133) sequences and 4,373 nucleotide alignments with 9 to 158 (average = 137) sequences.
Files and variables
File: omm_filtered_AA_CDS.tar
Description: Tar archive containing (amino acid) protein sequences in (gzip compressed) FASTA format.
File: omm_filtered_NT_CDS.tar
Description: Tar archive containing nucleotide gene sequences in (gzip compressed) FASTA format.
Code/software
Standard text software.
Access information
Data was derived from the following sources:
- OrthoMaM Database (https://orthomam.mbb.cnrs.fr)
Amino acid and nucleotide alignments were downloaded from OrthoMaM database version 12a for all genes with relative evolutionary rates greater than 1. Alignments were subset to the species present in the OrthoMaM species tree, sequences without ambiguities, and requiring the species Pan troglodytes, Pan paniscus, Homo sapiens, Gorilla gorilla, and Pongo abelii. Identical sequences were eliminated to ensure a bifurcating topology, resulting in 2,897 amino acid alignments with 9 to 156 (average = 133) sequences and 4,373 nucleotide alignments with 9 to 158 (average = 137) sequences.