How to keep a log of columns removed from edited MSA?

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6.9 years ago

DNAngel ▴ 250

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

MEGA MSA Python • 1.5k views

ADD COMMENT • link updated 6.8 years ago by Biostar 20 • written 6.9 years ago by DNAngel ▴ 250

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