Phylogenetic, dated tree of 138 Saccharomycetaceae

Species phylogeny of 138 Saccharomycetaceae, determined using a concatenation-based maximum likelihood analysis of 1,270 orthologous groups of proteins under a single LG+G4 model.This folder contains supermatrix_alignment_1270.phy - the concatenated, supermatrix alignment used to build the species treesupermatrix_alignment_1270.phy.iqtree - .iqtree file generated by IQ-TREE for the maximum-likelihood tree constructionspecies_tree_markers_used.txt - list of the markers used for species tree reconstruction. IDs taken from SGDFinalTree_1270AA_LG+G4.contree - the consesus tree file generated by IQ-TREEThe subfolder "tree_dating" containsalignment_random_subsampling.py = Python script used to subsample the alignment supermatrix_alignment_1270.physubsample_1_sequence.fasta = subsampled sequence used for the tree datingsites_subsampled_1.txt - list of sites from the supermatrix alignment included in the subsampled alignmentcalibrations_sceruva_scerklac.txt - Text file containing the calibrations used to date the species tree in the format needed for MEGA RelTimeMLreltime_ml_amino_acid.mao - specifications file for the MEGA RelTimeML analysis, as generated by the MEGA softwaresubsample_1_reltime_dated_summary.txt - log file for the MEGA analysis