I have many multifasta files with short sequences (100-200bp) . I would like to do a multiple sequence alignment between them. As the reads in in multifasta files are not in order, flirts they need to be placed in same order across all the fasta files and then perform MSA.
I have used
ProgressiveMauve for this purpose, but I am looking for any alternative tool.
ProgressiveMauve is good for large genomes, but I do not know how well it works for short sequences.