Phylogenetic tree based on CNV data

Question

[jsgounot]

Hi,

I would like to create an unrooted tree based on CNV data. Such trees were produced in other publication (like the S5 here) but I don't know which software to use and if I have to transform my data before. What's the best software to do that ? I looked at some but it looks like they only accept DNA alignments.

Thanks !

Answer 1

[ivivek_ngs]

It seems to me that the image is constructed with mega software. Take a look.

It is written below in the Supp fig legend:

Strains were clustered using the neighbor-joining algorithm on the Euclidian distances between the normalized average coverage values across all regions called as containing copy number variation within the species. The two trees are drawn to the same scale. Strain colors denote subpopulation origin

So I am assuming they computed a matrix of ED values for the regions with CNV having normalized coverage and clustering was done with NJ which is present in mega tool and then produced the figure.

You can take a look at this link for a software count however the link is broken but seems the thread was written 3 months ago so I believe it is temporary unavailability.

You can also take a look at CLIME

Answer 2

[jsgounot]

Thanks for the advises. In the end I have used SplitsTree with a distance matrix based on euclidean distances (phylip square matrix) and it works well !

[ivivek_ngs]

As long as it addresses your biological queries any tool is fine to fit your workflows, important is the interpretation. Good to know that you found something new and was able to address your own query. This will also be important for others in future.