Mostly Used (Fast) Global Pairwise Alignment Tool
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10.1 years ago
Pdubois ▴ 60

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?

alignment sequence dna • 5.8k views
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Entering edit mode
10.1 years ago
Neilfws 49k

There are lots - here's a Wikipedia list of pairwise alignment software.

I think MUMmer might do what you want.

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