ALE reconciliation files

Reconciliation of gene families for the 24 species genomic datasets
ml_reconciliations.tar.gz - ALE Maximum Likelihood reconciliations of gene families
Trees.tar.xz - ML tree files for all orthogroups
ALE_objects.tar.gz - ALE objects generated from tree files
alternative_root_trees.tar.gz - Alternative topologies used to test the likelihood of different root positions
dated_genome_tree.tre - dated species phylogeny against which gene trees were reconciled
alternartive_root_trees.tar.gz - alternative root positions tested using ALE
genome_alignment.phy - concatenated sequence alignment used to infer unrooted topology and divergence times
genome_set_input.txt - treefile with fossil calibration information for divergence time estimation
genome_dated_posterior.tre - treefile containing divergence times of genome-only phylogeny
genome_dated_posterior.txt - parameter output of divergence time analysis
in.BV - estimated branch lengths and Hessian matrix for divergence time analysis
WEREWOLF_loss.newick.txt - gene family phylogeny for WEREWOLF
WOX4_loss.newick.txt - gene family phylogeny for WOX4
STM_loss.newick.txt - gene family phylogeny for STM