splitMultiAlignments: splitMultiAlignments - split multiple alignments into...

In fmichonneau/chopper: Alignment Manipulations and Data Preparation for Phylogenetic Analyses

Description

Split a file containing multiple alignments into a multiple files.

Usage

splitMultiAlignments(file, prefix, pathin, pathout)

Arguments

file	the name of the file containing the multiple alignemnts to be split.
prefix	the prefix for each of the file name
pathin	path (i.e., directory) where the replicates for each locus are stored
pathout	path (i.e., directory) where the individual replicate for each locus are going to be stored.

Details

This function reads a file containing multiple alignments in the phylip format (as generated by seq-gen) and breaks each replicate into its own file. The files are named by putting together a prefix (specified by the user), the string ‘rep’ (stands for replicate), the replicate number, the name of the marker/locus (which should be part of the file name between an underscore and ‘.phy’, e.g., myalignment_marker.phy).

Value

TRUE, but really used for its side effect of generating individual alignment files.

Author(s)

Francois Michonneau

fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.