Data from: SimPhy: phylogenomic simulation of gene, locus and species trees

We present a fast and flexible software package—SimPhy—for the simulation
of multiple gene families evolving under incomplete lineage sorting, gene
duplication and loss, horizontal gene transfer—all three potentially
leading to species tree/gene tree discordance—and gene conversion. SimPhy
implements a hierarchical phylogenetic model in which the evolution of
species, locus, and gene trees is governed by global and local parameters
(e.g., genome-wide, species-specific, locus-specific), that can be fixed
or be sampled from a priori statistical distributions. SimPhy also
incorporates comprehensive models of substitution rate variation among
lineages (uncorrelated relaxed clocks) and the capability of simulating
partitioned nucleotide, codon, and protein multilocus sequence alignments
under a plethora of substitution models using the program INDELible. We
validate SimPhy's output using theoretical expectations and other
programs, and show that it scales extremely well with complex models
and/or large trees, being an order of magnitude faster than the most
similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can
be useful to understand interactions among different evolutionary
processes, conducting a simulation study to characterize the systematic
overestimation of the duplication time when using standard reconciliation
methods. SimPhy is available at https://github.com/adamallo/SimPhy, where
users can find the source code, precompiled executables, a detailed manual
and example cases.