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.