I want to compare genomes of two different species,but from the same genus. My motive is to find some different genes. what protocol or software can i use?
There are different ways to compare the gene content between two different genomes two examples:
1) A gene family analysis (http://en.wikipedia.org/wiki/Gene_family) can give you an idea about how genes that probably shared a common evolutionary history have been duplicated or removed in a specific species. The most used tool to perform a gene family analysis is OrthoMCL (http://orthomcl.org/orthomcl/). Once you have classify the genes by gene families other analysis can be done such as the evolution of the gene family using CAFE (http://sites.bio.indiana.edu/~hahnlab/Software.html). These analysis will let you know if there are specific duplications/losses of genes between the two species.
2) Synteny analysis can give you an idea about the reorganization of the different genes along the genome. Combined with the gene family analysis can be a very powerful tool to detect tandem duplications and gene clusters and genomic reorganizations. Again there are different tools, one example is SyMap (http://www.agcol.arizona.edu/software/symap/).
I hope this helps.
If you want to compare 2 or more genomes, Artemis Comparison Tools is what you need:
https://www.sanger.ac.uk/resources/software/act/
http://bioinformatics.oxfordjournals.org/content/21/16/3422.full
(it's free)
The best tool would depend on the amount of genes you wish to analyse. A different tool would almost certainly be required to analyse the difference between a human and chimpanzee vs two bacteria of the same genus, because of the size difference and splicing.
It also depends if you have already run ab initio gene prediction software, if not, this can be done with GeneMark (http://exon.gatech.edu/GeneMark/) or FGENESH (http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind). When you have the gff3 file of predictions, you can convert the genes to proteins (easiest way is to upload into GenSAS- https://www.gensas.org). You can use Roary on the GFF3 file to compare the pangenomes (https://sanger-pathogens.github.io/Roary/). Or you could use PROMPT (http://www.geneinfo.eu/prompt/) or OrthoMCL (https://orthomcl.org/orthomcl/) on the protein fasta to compare proteins or orthologous clusters of proteins respectively.
Hope this helps!
Good luck
Use Unipro Ugene software. It is free to use and very useful for such studies.
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