Remove non variable sites from sequence alignment

Question

[mglasena]

I'm looking for suggestions for programs that will remove nonvariable sites from a fasta/phylip/nexus alignment. I have very large sequence alignments, and I am hoping only to retain variable sites.

Answer 1

[Mensur Dlakic]

This will hopefully do what you want:

• https://research.pasteur.fr/en/software/bmge-block-mapping-and-gathering-with-entropy/
• https://ngphylogeny.fr/tools/tool/273/form