How to remove gaps from sequence alignment?

Question

[kapoornancy25]

I want to remove gaps from sequence alignment. How should do that is there any tools or software to do it or is it better to write a program and then proceed?

[cpad0112]

https://mothur.org/wiki/degap.seqs/

in python:

from Bio import SeqIO
import sys
from Bio import AlignIO

input_file = sys.argv[1]
output_file = sys.argv[2]

with open(output_file, "w") as o:
    for record in AlignIO.read(input_file, "fasta"):
        record.seq = record.seq.ungap("-")
        SeqIO.write(record, o, "fasta")

save it as python script. Run the script with input and output file names.

[liorglic]

Sorry, but your question is unclear. What do you mean by "remove gaps"? why would you want to do that? gaps are part of the alignment result...

[Dave Carlson]

If you literally remove all the gaps, it will no longer be an alignment. It will just be a multi-fasta file. Is that what you want? Or are you looking to remove positions/columns in the alignment file that include gaps? This would preserve the structure of alignment, at the cost of removing some information.

Answer 1

[h.mon]

If you want to remove sites with lots of gaps (thus inferred to be non-homologous), you can use gblocks or trimal.