Asslam u Alikum
I want to remove gaps from multiple sequence alignment , i tried many tools and scripts but it works in different ways.
H= -----ATGCGTACG-TGCA--C M= ATGCCCGATCGCH----ATC
I want to remove gaps according to reference like if gaps is present in first line (reference) remove that column like this
H= ATGCGTACGTGC M= CCCGATCGC----C
but different tools remove all gaps columns from whole file. please tell me any idea about it