Q:
I am writing to you reagarding ‘Pseudogenes’ detection within bacterial genome- I was wondering is there a software/ pipleline to use in order to identify pseudogenes within bacterial genome.

A:
The best way is to use our pseudogene annotation pipeline – Pseudopipe. You can download the stand-alone version that can be easily run on your computer and does not require a cluster:
http://pseudogene.org/pseudopipe/