Let me know if there is any software availble for that.
Basically I want to reduce the number of sequences prior to phylogenetic tree construction. The first step is to remove >90% identical sequences by cd-hit before multiple sequence alignment. Then I want remove the sequences which are >90% identical in the alignment. I am looking for a program for that purpose.
I use cd-hit to remove sequences by identity. However it does not work with multiple sequence alignments. So I wanted to know if there is software available for that.