Illustrates a typical workflow with GenPhyloData for generating a synthetic gene family. (a) A species tree is generated through a birth-death process over a given time interval. (b) A gene family is produced by letting an initial lineage evolve down to the leaves of the species tree by means of duplication, loss, lateral transfer and speciation events. The final gene tree is pruned of lost lineages. (c) The branch lengths of the clock-like gene tree are relaxed. (d) A multiple sequence alignment is created by applying a model of molecular sequence evolution over the relaxed gene tree.
Sjöstrand et al. BMC Bioinformatics 2013 14:209 doi:10.1186/1471-2105-14-209