Sequence Alignment editor suggestion

Question

[Alex S]

Hello guys!

I’m researching about repetitive sequences in plant species through bioinformatics approach’s. I have an alignment within a set of contigs. I wanna to divide these contigs into two groups related to they identity (or similarity obtained from the alignment). Anyone have a software suggestion (that runs multiple local alignment) and a path to divide these contigs?

I have tried the multiple local alignment using Geneious, UGENE, and MEGA but the mostly of them have only multiple global alignment. I tried to divided my alignment contigs using BioEdit and was no successful.

Bests

Answer 1

[GenoMax]

Have you tried JalView?

[N15]

I use Jalview as well - it's free, can be downloaded or launched through Java, and allows editing of alignments. You can color code by similarity and visually identify regions of similarity, and then manually divide. I am not sure whether there is an automated function to do this in Jalview.