I've been asked to align and manually edit some sequences for a phylogenetic analysis. I've aligned my data with ClustalW and MAFFT for comparison and spent several hours trying to figure out how to manually edit these alignments. I'm at a loss.
I thought I'd need trim the ends of the alignments to be read by MEGA, but my supervisor said I should just replace the gaps with Ns, and should look for misalignments. Since my supervisor is away for two weeks, I can't ask for any clarifications.
So, the questions are:
1) Is it a good practice to replace gaps with Ns and is there a certain way to do it? (Do I just replace all gaps with Ns, or only certain gaps?) 2) How do I identify misalignments? And do I delete the misaligned parts in one sequences or all? 3) If there is a good guide/workshop/tutorial on how to do manual editing, please refer me to it.