Entering edit mode
9.2 years ago
GouthamAtla
12k
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.
It's really difficult to answer your question because you have given us so little to go on -- where do these sequences come from? A single gene region, shotgun sequencing, etc.??? Are you assembling a genome? What are you trying to do?
The strategy you'll want to take will depend largely on what your research question is and the type of sequence data you have.
There are many tools for sequence alignment -- here's a pretty complete list of tools.
In any event, while you might be able to use Mauve for short regions, Mauve was designed for multiple genome alignments, so it doesn't sound like it is a good choice of a tool. Why did you decide this tool was a good choice for 100-200 bp sequences?