ips (version 0.0-7)

raxml: Maximum Likelihood Tree Estimation with RAxML

Description

This function calls RAxML (see Reference section) for the maximum likelihood estimation of tree topology and/or branch lengths for a given DNA sequence alignment, rapid and conventional non-parametric bootstrapping, mapping splits onto individual topologies, and a lot more. See the RAxML manual for details, especially if you are a new user of RAxML.

Usage

raxml(DNAbin, m, f, N, p, b, x, k, 
      partitions, outgroup, backbone = NULL, 
      file = "fromR", exec, threads)

Arguments

DNAbin

a matrix of DNA sequences of class DNAbin.

m

a vector of mode "character" choosing a model of subsitution; currently only GTR models available

f

a vector of mode "character" choosing from the RAxML algorithm analogous to the -f flag (see Detail section and RAxML manual).

N

either of mode "integer" or "character". Integers give the number of independant searches on different starting tree or replicates in bootstrapping. Alternatively, one of four bootstopping criteria can be chosen: "autoFC", "autoMR", "autoMRE", or "autoMRE_IGN".

p

integer setting a random seed for parsimony starting trees.

b

integer setting a random seed for bootstrapping.

x

integer setting a random seed for rapid bootstrapping.

k

logical, if TRUE the branch lengths of bootstrapped trees are recorded

partitions

a data frame specifying partitions of the alignment.

outgroup

a vector of mode "character" containing the names of the outgroup taxa.

backbone

a phylo object handed as a backbone tree to RAxML.

file

a vector of mode "character" giving a name to the output files.

exec

a vector of mode "character" giving the path to the directory containing the RAxML executable. The default value will work on Mac OS X if the folder containing the executale is renamed to "RAxML-8.0.3".

threads

integer giving the number of parallel threads to use (PTHREADS only).

Value

A list with a variable number of elements, depending on the analysis chosen:

"info"	RAxML log file as character string
"bestTree"	MLE of tree
"bipartitions"	MLE of tree annotated with bootstrap proportions
"bootstrap"	bootstrapped trees

Details

There are some limitations of this wrapper compared to RAxML run directly from the command line.

1. Only DNA is allowed as data type.

2. Option f can only take a limited number of values (d, a).

RAxML needs the specification of random seeds for parsimony estimation of starting trees and for bootstrap resampling. The corresponding argument names in raxml are identical to the flags used by RAxML (-p, -b, and -x). If you choose not to give any values, raxml will generate a (different) value for each requiered random seed every time it is called. Be aware that set.seed will work only for p, but not for b or x.

References

(in chronolocigal order)

Stamatakis, A., T. Ludwig and H. Meier. 2004. RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 1: 1--8.

Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688--2690.

Stamatakis, A., P. Hoover, and J. Rougemont. 2008. A rapid bootstrap algorithm for the RAxML web-servers. Syst. Biol. 75: 758--771.

Pattengale, N. D., M. Alipour, O. R. P. Bininda-Emonds, B. M. E. Moret, and A. Stamatakis. 2010. How many bootstrap replicates are necessary? Journal of Computational Biology 17: 337-354.

Stamatakis, A. 2014. RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics Advance Access.

See Also

raxml.partitions to store partitioning information in a data frame suitable for input as partitions argument in raxml.

Examples

# NOT RUN {
## bark beetle sequences
data(ips.cox1)
data(ips.16S)
data(ips.28S)

ips <- cbind(ips.cox1, ips.16S, ips.28S,
  fill.with.gaps = TRUE)

exec <- NULL # replace by your RAxML path

if ( !is.null(exec) ){

## normal tree search with GTRCAT and GTRGAMMA
tr <- raxml(woodmouse, f = "d", N = 2, p = 1234, 
            exec = exec) # -1743.528461
tr <- raxml(woodmouse, m = "GTRGAMMA", f = "d", N = 2, p = 1234, 
            exec = exec)

## rapid bootstrap
tr <- raxml(woodmouse, m = "GTRGAMMA",
            f = "a", N = 10, p = 1234, x = 1234, 
            exec = exec)

## rapid bootstrap with automatic halt
tr <- raxml(woodmouse, m = "GTRGAMMA", 
            f = "a", N = "autoMRE", p = 1234, x = 1234, 
            exec = exec)
}

# }