use GCG which is good and user friendly for gene annotation. its a commercial software.

Http://www.openbioinformatics.org/annovar/

Also You can try SnpEff.

Link : http://snpeff.sourceforge.net/

I used to work with Geneious (http://www.geneious.com/), which is very, very user-friendly. It's not free, however.

use GCG which is good and user friendly for gene annotation. its a commercial software.

Genome tools:

http://genometools.org/

VESPA: Integrates genomic and proteomic data

https://www.biopilot.org/docs/Software/Vespa.php

article ; http://www.biomedcentral.com/1471-2164/13/131

Geneious:

http://www.geneious.com/

JCVI : AAT;, eukaryotic annotation

http://aatpackage.sourceforge.net/

JCVI: Manatee ; bacterial

http://manatee.sourceforge.net/

try out link

http://www.jcvi.org/cms/research/software/

Here you can do almost things. Good luck..

For bacteria, there is the Microscope plateform. Process is free for academic research and it uses a web-based interface. To me the best annotation and comparative genomics sofwtare (and i have used many). It is free for academic, and you can have login to keep it private.

Check out: http://www.cns.fr/agc/microscope/mage/index.php.

For the services: http://www.cns.fr/agc/microscope/about/services.php?

For the viral genome, you could give Prokka (http://www.vicbioinformatics.com/software.prokka.shtml) a go, very fast and usually gives useful annotations.

O detect SNPs one ofmthe best is GATK. for genral procariotic genome annotation, might serve you wel ,for viruses, Bg7, Glimmer, Genmark.

Azizul Haque Md you can find here several useful links of software related to your work. Thank you