best way to compare two (or more) genoms

[NicoBxl]

Hi,

I wondered what is the best way to align two genomes. My goal is to annotate a newly sequenced genome with an annotated one.

Thanks,

N.

[shandley]

I am a big fan of MAUVE: http://gel.ahabs.wisc.edu/mauve/, but there are lots of other programs that do full genome alignment.

There is a presentation by Bill Pearson on the topic at: http://www.molecularevolution.org/mo..._galign_11.pdf

I have heard good things about MUGSY (http://mugsy.sourceforge.net/), but I am not sure that is the best option for your annotation needs. Plus it isn't as easy to install or work with as MAUVE.

Good luck!

SAH