Data from: Terrace aware data structure for phylogenomic inference from supermatrices

In phylogenomics the analysis of concatenated gene alignments, the
so-called supermatrix, is commonly accompanied by the assumption of
partition models. Under such models each gene, or more generally
partition, is allowed to evolve under its own evolutionary model. Though
partition models provide a more comprehensive analysis of supermatrices,
missing data may hamper the tree search algorithms due to the existence of
phylogenetic (partial) terraces. Here we introduce the phylogenetic
terrace aware (PTA) data structure for the efficient analysis under
partition models. In the presence of missing data PTA exploits (partial)
terraces and induced partition trees to save computation time. We show
that an implementation of PTA in IQ-TREE leads to a substantial speedup of
up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML
implementations, respectively. PTA is generally applicable to all types of
partition models and common topological rearrangements thus can be
employed by all phylogenomic inference software.