Did you tried MAFFT or MUSCLE?

try it, may be helpful.

http://www.ebi.ac.uk/Tools/msa/mafft/

http://www.ebi.ac.uk/Tools/msa/muscle/

you can also go for Clustalw (multiple sequence alignment)

JSpecies is the best way to do that. It is a nice java-based tool that gives you nice metrics about whole genome comparison based on BLAST, Mummer algorithms, and Kmers.

Hi Muhammed,

you might also have a look at Mauve:

http://darlinglab.org/mauve/mauve.html

It's pretty quick and easy generally for chromosome or small genome-sized (i.e., bacterial) comparisons.

Hi Muhammad,

have you tried dot plot?

gepard (http://bioinformatics.oxfordjournals.org/content/23/8/1026.full) is a user-friendly, java-based application  for quick creation of dot plots. It also works with large sequences.

good luck

Massimo

Hey Muhammad,

I agree with Massimo; a dot plot would be the way to go. Have you checked out CoGe? Your species may be on there and there are some really neat tools for comparative genomics.

https://genomevolution.org/coge/

Adam