Comparative Genomics - Make phylogenetic tree of species with available NCBI genomes

[dacotahm]

Hello,

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.

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=Nematocera

Thanks for any help!