MSCsimtester {MSCsimtester} | R Documentation |
Validity tests of simulators of the multspecies coalescent model in phylogenomics.
Description
The package performs comparisons of certain summary statistics for simulated gene tree samples to
theoretical predictions under the multispecies coalescent model.
The primary functions are rootedTriple
for comparison of frequencies of topological rooted triples
on gene trees, and pairwiseDist
and ADtest
for comparison of the distributions of pairwise
distances between taxa on gene trees.
Details
Required input is a collection of gene trees, stored as a multiPhylo
object by the ape
package,
and a rooted species tree, as a Phylo
object,
with edge lengths in generations, together with constant population sizes for each edge.
MSCsimtester
builds on the packages ape
and kSamples
.
For further examples of use and citation purposes, see Allman ES, Baños HD, Rhodes JA (2023). “Testing Multispecies Coalescent Simulators Using Summary Statistics.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(02), 1613-1618. ISSN 1557-9964, doi:10.1109/TCBB.2022.3177956..
Author(s)
Maintainer: Elizabeth Allman e.allman@alaska.edu [copyright holder]
Authors:
Hector Banos hbassnos@gmail.com [copyright holder]
John Rhodes j.rhodes@alaska.edu [copyright holder]
References
Allman ES, Baños HD, Rhodes JA (2023). “Testing Multispecies Coalescent Simulators Using Summary Statistics.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(02), 1613-1618. ISSN 1557-9964, doi:10.1109/TCBB.2022.3177956.