How to calculate distance matrix and phylogenetic tree for genome alignment
Hi, I have got some bacterial samples (total 10) and assembled using SPAdes. Now I am looking to generate phylogenetic analysis and metrics to show the percentage similarity. Please let me know if there is any way to generate metrics to show the percentage similarity. I tried Roary and RaXML for generating phylogenetic tree but I am not getting how to get metrics to show the percentage similarity among the samples.
Thank you!
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This paper on PMC from 2019 deals specifically with whole-genome alignment, maybe it also contains helpful hints to software that might support this.
It has headings Multiple genome alignment tools and Pairwise genome alignment tools, so I guess you should find something there.
Also it contains a brief introduction and review of the set of methods you are going to use.
This paper assesses some methods for full-genome phylogenies, I figure you could easily find one that has a broader review character still.
Maybe this list contains some helpful inspiration too.
I used Mugsy, progressiveMauve and Mauve. However, I could not find the distance matrix to show the percentage similarity.