raxml.partitions: Partition scheme for RAxML

In ips: Interfaces to Phylogenetic Software in R

Partition scheme for RAxML

Description

Given a set of DNA sequence alignments, raxml.partitions creates a data frame with partition bounderies that can be input into raxml.

Usage

raxml.partitions(...)

Arguments

...	Two or more DNA sequence alignments of class DNAbin.

Details

For raxml.partitions to make sense, the DNA sequence alignments must be given exactly in the same order in which they are concatenated into a supermatrix (see Examples section). Without any testing, the type of sequences is supposed to be DNA.

Value

A data frame with four columns (type, locus, begin, and end) and number of rows corresponding to the number of partitions.

See Also

cbind.DNAbin to concatenate multiple alignments; raxml for an interface to RAxML.

Examples

## bark beetle sequences
data(ips.cox1)
data(ips.16S)
data(ips.28S)

## Note the same order of individual
## alignments in both functions:
## ----------------------------
raxml.partitions(cox1 = ips.cox1, 
                 r16S = ips.16S, 
                 r28S = ips.28S)

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

ips documentation built on May 29, 2024, 4:39 a.m.