HyPhy: Macroevolutionary phylogentic analysis of species trees and gene trees

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A Bay Area high level phylogenetic analysis package mostly using the birth-death process. Analysis of species tree branching times and simulation of species trees under a number of different time variable birth-death processes. Analysis of gene tree species tree reconciliations and simulations of gene trees in species trees.

Author
Nathaniel Malachi Hallinan
Date of publication
2012-07-30 04:09:01
Maintainer
Nathaniel Malachi Hallinan <nmhallinan@gmail.com>
License
GPL-2
Version
1.0

View on CRAN

Man pages

get.recon.1
Internal Functions
HyPhy-package
Macroevolutionary phylogentic analysis of species trees and...
recon.score
Duplications and losses for gene tree in a species tree
requiprobable
Sample trees from an equiprobable labeled, semi-labeled or...
rgenetree
Samples gene family trees that evolved on a species tree with...

Files in this package

HyPhy
HyPhy/MD5
HyPhy/R
HyPhy/R/rgenetree.R
HyPhy/R/requiprobable.R
HyPhy/R/recon.score.R
HyPhy/R/get.recon.1.R
HyPhy/NAMESPACE
HyPhy/man
HyPhy/man/rgenetree.Rd
HyPhy/man/requiprobable.Rd
HyPhy/man/recon.score.Rd
HyPhy/man/HyPhy-package.Rd
HyPhy/man/get.recon.1.Rd
HyPhy/DESCRIPTION