Mostly Used (Fast) Global Pairwise Alignment Tool

Question

[Pdubois]

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?

Answer 1

[Neilfws]

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

I think MUMmer might do what you want.