phylogenetic tree construction using scaffolds of genome against specific gene of interest

Question

[noobiestar]

Hi, I have multiple bacterial genomes (with long scaffolds). I would like to construct a phylogenetic tree of these bacteria with a specific gene of interest from a reference genome. How should I approach to this problem? What if I take only the largest contig from the bacterial genomes and try to make phylogenetic tree. I tried MEGA, but could not even finish multiple sequence alignment. Any suggestions would be appreciated. I am new to bioinformatics.

Answer 1

[Mensur Dlakic]

Generally speaking, you don't align complete bacterial genomes. Most alignment methods don't align sequences with a length in hundreds of thousands residues (or millions). Besides, there are methods that will give you fairly accurate identity percentage between genomes in much less time:

https://github.com/ParBLiSS/FastANI

If you need to make phylogenetic trees, a better approach is to align several representative proteins, concatenate the alignments, and make a tree from that super-alignment. I recently described that in more detail here.