To remove the gaps or keep the gaps in 16s multiple alignment for phylogeny using RAXML?

Question

[senguptashruti]

I am working with 16S sequences and want to build phylogeny. After building the multiple alignments using MEGA, the alignment is showing gaps. I do not want to remove any sequence. Some papers suggesting to remove the gaps by setting tolerance to 75% and some suggesting not needed. Can I remove the gaps manually without losing information?

[Joe]

I believe I'm right in saying that (at least the recent implementations of) RAxML will automatically discard low information sites (i.e. majority gap columns). Assuming your alignment is otherwise decent quality I don't think you need to manipulate it any further, but I would double check with the software manual specifically.