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 

I second Sascha's recommendation that you stick with Geneious. Their support is second to none in my experience - if you are having issues I would talk to them.

Geneious has become my primary tool for nucleotide alignment, curation and viewing. It handles large alignments very well. Their phylogenetic tools aren't bad either depending on what you're after (I find the Bayesian plug-in a bit inefficient when compared to the command line variant).

Thank you all. Support from Geneious team helped me to sort it out.