Remove invariant sites from large MSA

Question

[lkatz]

I am looking for a Python or other script (or software package) to remove invariant sites from a large nucleotide multi-sequence alignment. Essentially, I am working towards creating a birds-eye view of variable sites among individuals. I'd appreciate any advice.

Answer 1

[virtualinterlect]

You can try this "Script for removing or counting invariant sites for the RAxML ascertainment bias corrections"

https://github.com/btmartin721/raxml_ascbias

Answer 2

[Mensur Dlakic]

BMGE is an entropy-based method that will automatically select the columns that are most informative. It does so in blocks, so individual conserved residues surrounded by variable columns may not be removed.