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Updated: May 10, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
GenPhyloData: realistic simulation of gene family evolution
Joel Sjöstrand1, Lars Arvestad, Jens Lagergren
1Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.
Background:
PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock.
Result:
Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data.
Conclusion:
The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.
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