genetreeSample {MSCsimtester}

Simulated gene tree dataset.

Description

A dataset of 10,000 gene trees on 5 taxa simulated under the MSC on a species tree.

Format

A text file with 10,000 metric Newick gene trees on the taxa a,b,c,d,e

Details

This simulated dataset was produced by SimPhy (Mallo et al. 2016), using the species tree

((((a:10000,b:10000):10000,c:20000):10000,d:30000):10000,e:40000);

with population sizes

c(15000,25000,10000,1,1,1,1,1,12000)

and edges ordered by the ape function read.tree.

File is accessed as system.file("extdata","genetreeSample",package="MSCsimtester"), for example using the ape command:

gts=read.tree(file=system.file("extdata","genetreeSample",package="MSCsimtester") )

References

Mallo D, De Oliveira Martins L, Posada D (2016). “SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.” Syst. Biol., 65(2), 334-344. doi: 10.1093/sysbio/syv082, http://dx.doi.org/10.1093/sysbio/syv082.