completeSeqWithGaps: Complete sequences with gaps.

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

Description

Standardize the lengths of the sequences in a FASTA file by adding gaps (or other characters) at the end.

Usage

completeSeqWithGaps(file, output, format = "fasta", colsep = "",
  gaps = "-", ...)

Arguments

file	input file in the FASTA format or other format that can be read by ape:::read.dna
output	path and name file for the output.
format	format fo the input file, to be passed to ape:::read.dna
colsep	a character used to separate the columns
gaps	character to be as gap
...	further arguments to be passed to ape:::write.dna to format the output file.

Details

This function takes an alignment in which the sequences are of different lengths (for instance, if 2 alignments are concatenated manually), and standardizes the lengths by adding gaps at the end of the sequences. If you want the output file to be aligned, you need to make sure that the sequences are otherwise aligned (they only differ by some gaps at their extremities).

Value

TRUE. This function is intended to be use for its side effect which create a new alignment file with standardized sequence lengths.

Author(s)

Francois Michonneau

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