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

Question

[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.

Link to the specific NCBI page

Thanks for any help!

[GenoMax]

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?

[dacotahm]

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

[yousefifariba6]

Hi. I have problem in trimmomatic: Exception in thread "main" java.lang.NumberFormatException: For input string: "10‬‬" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.base/java.lang.Integer.parseInt(Integer.java:652) at java.base/java.lang.Integer.parseInt(Integer.java:770) at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:56) at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32) at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:303) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

[Carambakaracho]

How do you think this relates to the original question?

Answer 1

[Mensur Dlakic]

To download genomes:

https://github.com/kblin/ncbi-genome-download

To build a concatenated tree from single-copy genes:

https://github.com/yuwwu/ezTree

ezTree is meant for prokaryotes, but it is not difficult to modify it so it works with eukaryotic genomes. Not sure if you want to deal with that, though.

You can always use BUSCO to identify single-copy genes present in all or most of your species of interest, then concatenate the alignments and build a tree manually.

Answer 2

[Juke34]

You can use ncbi_get_genome_tree.pl from the GAAS toolkit. It creates a tree in nh format.

e.g for all mammals genomes available (where 40674 is the mammals taxid):

ncbi_get_genome_tree.pl -t 40674

Answer 3

[fconstancias]

Check the excellent GToTree software https://github.com/AstrobioMike/GToTree