ALE reconciliation files

Reconciliation of gene families for the 24 species genomic datasetsml_reconciliations.tar.gz - ALE Maximum Likelihood reconciliations of gene familiesTrees.tar.xz - ML tree files for all orthogroupsALE_objects.tar.gz - ALE objects generated from tree filesalternative_root_trees.tar.gz - Alternative topologies used to test the likelihood of different root positionsdated_genome_tree.tre - dated species phylogeny against which gene trees were reconciledalternartive_root_trees.tar.gz - alternative root positions tested using ALEgenome_alignment.phy - concatenated sequence alignment used to infer unrooted topology and divergence timesgenome_set_input.txt - treefile with fossil calibration information for divergence time estimationgenome_dated_posterior.tre - treefile containing divergence times of genome-only phylogeny genome_dated_posterior.txt - parameter output of divergence time analysisin.BV - estimated branch lengths and Hessian matrix for divergence time analysisWEREWOLF_loss.newick.txt - gene family phylogeny for WEREWOLFWOX4_loss.newick.txt - gene family phylogeny for WOX4STM_loss.newick.txt - gene family phylogeny for STM