Hello Sanjay Gautam, if you'd like to keep going with Geneious you may should consider asking your questions at the Geneious support forum:

https://support.geneious.com/forums

Here, also employees respond to your questions, but you should provide more info on your data set (genome size, how you've set up the alignment, which geneious version are you using,...). And if you'd like to do comparative genomics by aligning whole genomes I'd rather suggest the MAUVE aligner, which is also available as plugin.

Good luck,

Sascha 

What format is your sequence data in? I've found MEGA6 to be one of the most effective and easy to use. 

Mega7 is out but have heard it has some glitches. 

Hello Sanjay Gautam, if you'd like to keep going with Geneious you may should consider asking your questions at the Geneious support forum:

https://support.geneious.com/forums

Here, also employees respond to your questions, but you should provide more info on your data set (genome size, how you've set up the alignment, which geneious version are you using,...). And if you'd like to do comparative genomics by aligning whole genomes I'd rather suggest the MAUVE aligner, which is also available as plugin.

Good luck,

Sascha