I am working with a 100 complete M. tuberculosis genomes in FASTA format. What I want to do is align all the sequences to search for common genomic regions between all the strains. MAUVE was the only program that I found that could handle this big set of data. Any ideas on how to generate a consensus sequence with these common genomic regions from MAUVE? Is there any other program that can handle such big data and make a consensus sequence? I tried PhyDE but MUSCLE could only align a tiny initial portion of the genome. PhyDE would haven been ideal since it can align and make a consensus sequences, but it does not even work with two whole genomes.
Appreciate the attention.