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.
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written
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noobiestar •
1 answer
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.
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