Filtering repetitive sequences from MAF files

Question

[adam.carol]

Hello!

Is there any available tool to remove repetitive sequences from genome alignments (MAF format)? The fasta files used in the alignments were downloaded from NCBI and were already masked, but for some reason I still have a lot of repetitive sequences in the resulting MAF files (maybe microsatellites?). I'd like to avoid masking the fasta files with another tool because I'm using the whole genome sequence of more than 90 species and it would take a gigantic amount of time. Processing the maf files would be less time consuming.

Thanks!

Answer 1

[yudizhang628]

I have the same problem, did you solve it?