Visualise node-defining SNPs on a phylogeny

Question

[tim_mci]

Hi all,

I have an alignment in fasta format and a phylogenetic tree in Newick format. I am looking for a way to visualise/map the character state changes or SNPs to the node/branches they define. Any suggestions on available software that does this?

Thanks in advance, Tim.

Answer 1

[natasha.sernova]

What organism are you working with?

In case of bacteria, there several tools and papers about them:

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429496/

Displaying data associated with phylogenetic trees - there is a comparison of many tools

https://bacpathgenomics.wordpress.com/2012/05/25/displaying-data-associated-with-phylogenetic-trees/

Again bacteria:

http://nar.oxfordjournals.org/content/early/2016/04/29/nar.gkw359.full

In case of humans or viruses:

Whole genome single-nucleotide variation profile-based phylogenetictree building methods for analysis of viral, bacterial and human genomes

http://www.sciencedirect.com.sci-hub.cc/science/article/pii/S0888754314000949

or this one:

Population structure: GST, genetic distance, and clustering

http://grunwaldlab.github.io/Population_Genetics_in_R/Pop_Structure.html

Answer 2

[tim_mci]

Thank you heaps for that, it should help with my human mtDNA data!