gapless_msa {orthGS}R Documentation

Remove Gaps in a MSA

Description

Removes gaps in a given msa.

Usage

gapless_msa(msa, seqtype = 'AA', df = TRUE, sfile = FALSE)

Arguments

msa

input alignment.

seqtype

the nature of the sequences: 'DNA' or 'AA'.

df

logical. When TRUE msa should be a matrix, when FALSE msa should be a string giving the path to a fasta file containing the alignment.

sfile

if different to FALSE, then it should be a string indicating the path to save a fasta alignment file.

Details

It should be noted that this function does not carry out the alignment itself.

Value

an alignment without gaps in form of matrix or a file containing such an alignment in fasta format.

See Also

msa

Examples

## Not run: gapless_msa(msa(sequences = c("APGW", "AGWC", "CWGA"),ids = c("a", "b", "c"))$ali)

[Package orthGS version 0.1.8 Index]