run.seqgen: run seq-gen
In lliu1871/phybase: Basic functions for phylogenetic analysis

run.seqgen

R Documentation

run seq-gen

Description

The function runs seq-gen

Usage

run.seqgen(path_seqgen="./Seq-Gen-1.3.4/seq-gen",nsim=1, seed=123, basefreq=rep(0.25,4), rate=rep(1,6), seqlength=1000, gamma=0, inv=0, treefile, saveformat="phylip", outputfile)

Arguments

`path_seqgen`	the path of seqgen
`nsim`	The number of simulations. All simulated data are saved to the same outputfile
`seed`	the random seed
`basefreq`	base frequencies
`rate`	six relative rates in the rate matrix
`seqlength`	the length of simulated sequences
`gamma`	the gamma parameter
`inv`	the proportion of invariant sites
`treefile`	the file of the true tree
`saveformat`	phlip, nexus, or fasta
`outputfile`	the simulated sequences are saved to outputfile