Question: How to keep a log of columns removed from edited MSA?
0
gravatar for DNAngel
22 months ago by
DNAngel40
DNAngel40 wrote:

I have used several programs like MEGA7, Mesquite, and even tried a python script that allows me to edit MSA by deleting very gapped columns (by codon). Now, I need to do this for well over 200 different MSAs for different species and I cannot find a program or an R package or even python package that will keep a record of which columns were removed. It is hard for me to edit the python script because every time one column is removed, the indices change. Is there a program that will keep track of the columns removed so that I can go back and see why it was removed?

For example, assuming these are in codons:

sp1 AL---Y

And say based on the rest of the alignment, I delete the last 4 columns here. I would need it tracked in some way. An idea is below:

Removed Columns:

sp1 Codon 3: - Codon 4: - Codon 5: - Codon 6: Y

Or anything similar

msa mega python • 447 views
ADD COMMENTlink modified 21 months ago by Biostar ♦♦ 20 • written 22 months ago by DNAngel40

Please provide a sample of one of the input MSA files and the desired output file.

ADD REPLYlink modified 22 months ago • written 22 months ago by Vincent Laufer1.1k

Have you tried Gblocks?

ADD REPLYlink written 21 months ago by Sej Modha4.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 976 users visited in the last hour