Question: Comparative Genomics - Make phylogenetic tree of species with available NCBI genomes
gravatar for dacotahm
2.6 years ago by
United States
dacotahm10 wrote:


I'm doing some comparative genomics and NCBI's taxonomy browser is useful for screening species with genomes available. I want to export this in Newick or some standard format so I can visualize it easily in R or ITOL.

There isn't a mechanism to export a list though...

Is there a method that doesn't take much time to pull species or IDs from NCBI that have published genomes and create an exportable tree? I don't do this often enough to know many of the resources.

Specifically, I want a tree of all the species in Nematocera which have genomes.

Link to the specific NCBI page

Thanks for any help!

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by dacotahm10

One would need to pick a gene that is present in all those genomes and build a tree after doing a MSA, correct? Or are you only looking to get a tree-like representation of the information on the page you linked?

ADD REPLYlink written 2.6 years ago by genomax69k

The second - Lets say I want to build a tree of all Dipterans for which NCBI has a genome available. That linked page shows the list of species screened for genome, and the phylogeny for each species. I would like to find a way to access that information and export it as a Newick or some other format I can use to build visuals.

This website can access NCBI phylogenetic information, but I would like to find out how to screen out only the species in a clade with genomes

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by dacotahm10
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