02_hypothesis_trees

Constraint treesCompressed directory of constraint trees for 14 empirical phylogenetic datasets, for the 5 most common hypotheses of animal evolution. Constraint trees are used to set restrictions on tree topology in tree estimation. Note that Placozoa species were not constrained, as the placement of Placozoa is not resolved. constraint_tree_1 - Ctenophora-sister, Porifera monophyletic: (Outgroup, (Ctenophora, (Porifera, (Cnidaria, Bilateria))))constraint_tree_2 - Porifera-sister, Porifera monophyletic: (Outgroup, (Porifera, (Ctenophora, (Cnidaria, Bilateria))))constraint_tree_3 - (Ctenophora+Porifera)-sister, Porifera monophyletic: (Outgroup, ((Ctenophora, Porifera), (Cnidaria, Bilateria)))constraint_tree_4 - Ctenophora-sister, Porifera paraphyletic: (Outgroup, (Ctenophora, ((Calcarea, Homoscleromorpha), ((Hexactinellida, Demospongiae), (Cnidaria, Bilateria)))))constraint_tree_5 - Porifera-sister, Porifera paraphyletic: (Outgroup, ((Calcarea, Homoscleromorpha), ((Hexactinellida, Demospongiae), (Ctenophora, (Cnidaria, Bilateria)))))Porifera clades: Calcarea, Homoscleromorpha, Hexactinellida, DemospongiaeMonophyletic Porifera topology: (Calcarea, Homoscleromorpha, Hexactinellida, Demospongiae) Hypothesis treesCompressed directory of IQ-Tree output files (log, iqtree, and tree files) for constrained maximum likelihood tree estimation for 14 empirical phylogenetic datasets.Contains four subfolders, one for each class of model:Single - single matrix amino acid substitution models (e.g., LG and WAG)Mixture - mixture models from in IQ-Tree (e.g., LG4M and UL2)PMSF - PMSF approximation of C20 and C60 modelsCXX - the C20 and C60 modelsFor each of the 14 datasets, we identified the best model in each class and estimated 5 constrained trees with the 5 most common hypotheses of evolution.