computePhylo: Compute Phylogeny

In iferres/phylen: Search Core Genes Using HMMs, Compute Multiple Alignment, Concatenate And Compute Phylogeny

Description

Takes the core genes alignment and produce a phylogeny.

Usage

computePhylo(ali, mode = "ml", nbs = 100L, n_threads = 1,
  outPrefix = "phylo", outDir = ".", rearrangement = "NNI", ...)

Arguments

ali	The path to the alignment file.
mode	One of "nj" (Neighbour-joining) of "ml" (Maximum likelihood).
nbs	The number of bootstraps.
n_threads	The number of cpus to use. Just used if nbs > 0.
outPrefix	A prefix to use on the output files.
outDir	Where to put the newick files.
rearrangement	Choice of tree rearrangement, only used if mode="ml".
...	Further arguments to pass to optim.pml.

Details

Takes the core gene alignment and produces newick files. If mode is set to "nj", the outfile will have a "_nj.nwk" subffix. If set to "ml" and nbs = 0L, then it will be "_ml.nwk", and if "ml" and nbs > 0L, then it will output a second file with the bootstrap trees with the suffix "_ml_nbs.nwk".

Multiple cpus can be used when performing bootstrap.

It uses the "GTR" model to optimize the tree.

Value

An object of class "phylo" (phangorn and ape packages), and the specified newick files.

Author(s)

Ignacio Ferres

References

Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290. Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593.

iferres/phylen documentation built on May 24, 2019, 2:04 a.m.