concatenateAlignments: Concatenate alignments

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

Description

Concenate marker alignements to generate a single alignment.

Usage

concatenateAlignments(pattern, path, output, input.format = "fasta",
  partition = NULL, partition.format = c("raxml", "nexus"),
  create.conc = TRUE, standardize = FALSE, drop = NULL, ...)

Arguments

pattern	character string to identify aligned files in folder
path	path where the alignment files are to be found
output	file name (with full path) for the concatenated file
input.format	format of the input DNA alignment (to be passed to ape:::read.dna)
partition	if NULL no partition file is created, otherwise a character string indicating the file name where to write the partitions
partition.format	which format should be used to create the partition file (raxml or nexus)
create.conc	if TRUE create the concatenated file, if FALSE useful for testing (dry run) or to create partition file
standardize	not needed if alignments created by ‘mergeSeq’. Otherwise the alignments names are standardized for each of the individual markers by generating empty sequences.
drop	a character vector indicating the sequences that need to be removed from the output
...	further arguments to be passed to write.dna for the output file

Details

Given a series of files generated by ‘mergeSeq’, this function creates an alignment from these files. WARNING: the files for the independent loci are assumed to be created using the function mergeSeq, meaning that the loci is indicated in 3rd position, separated by an hyphen e.g. 20120808-101010-COI.fas

Value

This function is used for its side effect of creating an alignment from a set of alignemnts (marker based). It can also create a partition file that can added at the end of the alignment to specify where each marker starts and ends.

Author(s)

Francois Michonneau

Examples

## Not run: 
concatenateAlignments(pattern="^20121017-112755.+afa$", path="/tmp/seq",
                      output="/tmp/seq/20121017.impatiens.fas",
                      partition="/tmp/seq/20121017.impatiens.part",
                      partition.format="nexus", colsep="", colw=10000)

## End(Not run)

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