Phylogenetic analysis of the gain/loss of genes along different species lineages?

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António Amorim

I am not sure to understand your question, but first clarify if you mean genes (active) or sequences (pseudogenes and alike)

Ramanandan Prabhakaran

Thanks Dr.Antonio. I have updated the query. Please let me know about it.

Well - then it means you have (access to) a collection of reliable whole genomes for each of these strains/species. Is that so?

Yes I have a set of genomes and their corresponding annotated genes & tRNA genes as well in a file.