Raw data for Mirarab et al. 2024 in PNAS: "A region of suppressed recombination misleads neoavian phylogenomics"

Supplementary data repository for the study by Mirarab et al. 2024 in PNAS: "A region of suppressed recombination misleads neoavian phylogenomics".

This repository includes raw data used from the companion paper based on the Stiller et al. 2024 study (in press in Nature). The main analysis from this study is based on 63430 loci obtained from intergenic regions, maximum likelihood analysis, and coalescent-based species tree estimation, which are included in this repository.

For more data analyses specific to this paper, please refer to https://zenodo.org/records/10699424

Files and explanation of content:

* 63430.alignments.tar.gz Alignments in FASTA format for which gene trees were built

* 63430.gene.trees.gz Gene trees in newick format with support as aLRT values.

* 63430.aLRT-0.95-collapsed.gene.trees.gz 63430 gene trees after collapsing branches with aLRT values below 0.95. This file was used as input for ASTRAL analysis.

* 63430.named.gene.trees.gz Gene trees, with 1st column is name of the underlying locus, 2nd column is tree in newick format in order to match gene trees to alignments.

* 63430.aLRT-0.95-collapsed.gene.trees.gz

* 63430.ASTRAL.species.tre Main species tree resulting from ASTRAL analysis.

* 63430.timetree.tre The time calibrated species tree.