README.md

In emanuelmfonseca/P2C2M.GMYC: Model violations under the Generalized Mixed Yule Coalescent (GMYC)

P2C2M.GMYC

** under development **

An r-package for identifying model violations under the Generalized Mixed Yule Coalescent (GMYC) model

Installation:

P2C2M.GMYC can be installed from Github using the function install_github implemented in devtools R-package.

library(devtools)
devtools::install_github("emanuelmfonseca/P2C2M.GMYC")

P2C2M automatically installs all the dependencies, but if you get errors, try to install them individually. Here is the list of all required packages:

install.packages("ape") install.packages("pegas") install.packages("phangorn") install.packages("phyclust") install.packages("pegas") install.packages("TreeSim") install.packages("splits", repos="http://R-Forge.R-project.org", type="source") install_github("liamrevell/phytools")

Example:

To run the parametric bootstrap version of the P2C2M.GMYC, users need to provide an ultrametric phylogenetic tree and a sequential fasta alignment.

Lygodactylus ssp. – Lanna et al. (2018)

We included Lygodactylus dataset in P2C2M.GMYC as an example. The Lygodactylus dataset includes 66 sequences of the mitochondrial ND4 gene for 19 described species. This dataset was chosen for representing a typical dataset used in GMYC analysis, where each species can be represented from one to many sequences. So, we will investigate if the GMYC model is a good fit for the evolutionary history of Lygodactylus* ssp. using the parametric bootstrap version.

library(P2C2M.GMYC)

P2C2M_GMYC.Pboot(tree.input=system.file("extdata", "Lygodactylus.tre", package="P2C2M.GMYC"),
                 tree.format="nexus",
                 seq=system.file("extdata", "Lygodactylus.fas", package="P2C2M.GMYC"))

Results can be accessed in P2C2M_GMYC.results object.

P2C2M_GMYC.results

Reference:

Lanna, F.M., Werneck, F.P., Gehara, M., Fonseca, E.M., Colli, G.R., Sites-Jr., J.W., Rodrigues, M.T., and Garda, A.A. 2018. The evolutionary history of Lygodactylus lizards in the South American open diagonal. Molecular Phylogenetics and Evolution, 127: 638–645. https://doi.org/10.1016/j.ympev.2018.06.010

emanuelmfonseca/P2C2M.GMYC documentation built on Aug. 30, 2020, 5:20 a.m.