How to calculate distance matrix and phylogenetic tree for genome alignment
0
0
Entering edit mode
6 weeks ago
Kumar ▴ 120

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!

distance phylogenetic Genome tree matrix • 270 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

I used Mugsy, progressiveMauve and Mauve. However, I could not find the distance matrix to show the percentage similarity.

ADD REPLY

Login before adding your answer.

Traffic: 1828 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6