Comparing two fasta contig files

[budgie lover]

Hi everyone,

I am trying to find out statistical information for two fasta files that contain contigs. I am mostly concerned about matching contigs and contigs that do not match. I ran the data through CD-HIT which outputted a fasta file with all of the matching sequences. Can someone point me in the right direction by suggesting a software that can help me learn more from this data?

Thank you.

[maubp]

For visual assembly comparison, you could try mummer plot, or ACT (Artemis Comparison Tool).