How Does Multiple Genome Alignment Work?

Question

[nelson.liu.2009]

Hi Everyone,

I'm wondering how multiple genome alignment works. From what i've read, an algorithm goes through all the genomes and finds matching regions between all of them. How do they use these matching regions to infer the path that evolution took to differentiate the species?

Answer 1

[linus]

Here is a paper about Mauve. I think one of the most used multi-genome aligners. In the "Methods" section they write how their algorithm works.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC442156/

I hope it is not behind a paywall.