Phylogenomic data for Herranz et al.

The repository contains:

0_OrthoFinder_MultipleSequenceAlignments.tar.gz: orthogroup alignment files as produced from OrthoFinder.

1_OrthoFinder_GeneTrees.tar.gz: gene trees obtained for orthogroup alignments as produced by OrthoFinder using FastTree.

2_OrthoFinder_ResolvedGeneTrees.tar.gz: rooted and resolved gene trees as produced by OrthoFinder.

3a_PhyloTreePruner_SingleCopyAlignments_GeneTrees.tar.gz: Single copy alignments as generated by PhyloTreePruner from the Resolved Gene trees and the Multiple Sequence Alignments. After pruning, alignments were realigned with MAFFT L-ins-i. Gene trees obtained from the realigned single copy gene trees with IQTREE.

3b_ASTRAL_SingleCopySpeciesTree.tar.gz: Input and output files of ASTRAL-III species tree analysis.

3c_IQTREE_Supermatrices.tar.gz: Input and output files of concatenated species tree analysis based on the 70% and 80% occupancy matrix analyzed with IQTREE.

4_ASTRAL-Pro_MultiCopySpeciesTree.tar.gz: Input and output files of ASTRAL-Pro species tree analysis, which analyzed multi copy gene trees from OrthoFinder (1_OrthoFinder_GeneTrees.tar.gz) to build a species tree.

5a_ASTRAL-Pro_noLowQuality.tar.gz: input and output files for ASTRAL-Pro species tree analysis after removing lower quality transcriptomes (E. dujardinii, E. kohni, Pycnophyes sp.).

5b_ASTRAL-Pro_noOutgroups.tar.gz: input and output files for ASTRAL-Pro species tree analysis after removing the transcriptomes of the long branched Nematoida and Loricifera.