dataGeneTreeSample {MSCquartets}

Simulated gene tree dataset from species tree

Description

A text file dataset containing 1000 gene trees on 9 taxa simulated under the MSC on a species tree

Format

A text file with 1000 metric Newick gene trees on the taxa t1-t9

Details

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

((((t5:5000,t6:5000):5000,t4:10000):2500,t7:12500):7500,((t8:3000,t9:3000):5000,
((t1:4000,t2:4000):2500,t3:6500):1500):12000);

with a population size of 10,000 throughout the tree.

File is accessed as system.file("extdata","dataGeneTreeSample",package="MSCquartets"), for example via the ape command:

gts=read.tree(file = system.file("extdata","dataGeneTreeSample",package="MSCquartets") )

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.