simSeqfromSp2: simSeqfromSp2: Modified function of simSeqfromSp from R...

In radamsRHA/Misc.Statistics.Genetics.Models:

Description

The function simulates sequences from a species tree.

Usage

simSeqfromSp2(sptree, spname, ntaxasp, ngene, theta = 0, noclock = 0,
  simsequence = 1, murate = "Dirichlet", alpha = 5, seqlength = 100,
  model = 1, kappa = 2, rate = c(1, 1, 1, 1, 1, 1), frequency = c(1/4,
  1/4, 1/4, 1/4), outfile, format = "phylip")

Arguments

sptree	A species tree which must be a rooted tree.
spname	species names
ntaxasp	a vector of the number of individuals in each species
ngene	number of genes
theta	population size
noclock	0: clocklike species tree 1: nonclocklike species tree
simsequence	1: simulate sequences and gene trees, 0: simulate gene trees
murate	distribution of mutation rates
alpha	the shape parameter of dirichlet distribution
seqlength	the number of nucleotides along the sequences
model	substitution model
kappa	transition/transversion ratio
rate	rates
frequency	nucleotide frequency
outfile	the full path of the output file
format	either "phylip" or "nexus"

radamsRHA/Misc.Statistics.Genetics.Models documentation built on May 5, 2019, 6:56 p.m.