Tool For Multiple Sequence Alignment Of Genomes

Question

[GouthamAtla]

I would like to know the good tools for multiple sequence alignment of genomes accross species to find out the conserved sequences ( For ex..human, rat, mouse etc ). I came across the tools like Multi-LAGAN, Threaded Blockset Aligner, BFAST Others..etc Before testing them..I would like to take suggestions from here. And if any one has done this kind of work, I would appreciate any suggestions from them. Computational power is not a limitation for us.

[Konrad]

Have you seen Mauve?

[GouthamAtla]

@Konrad...Thanks a lot for your suggestion. Mauve is good but somehow i am unable to run it. Finally I am using Mummer (nucmer) and SyMap ( Which internally calls nucmer, promer etc ) and it is simple to use. SyntenyMiner also seems to be a good choice to visualize the nucmer output.