Mostly Used (Fast) Global Pairwise Alignment Tool
I am trying to align contigs to several chromosomes in genome using global alignment (i.e. query and reference files contain multiple fasta entry).
I looked at EMBOSS' needle but it is too slow.
Is there any practical tool for such task?
1 answer
There are lots - here's a Wikipedia list of pairwise alignment software.
I think MUMmer might do what you want.
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