Question: Phylogentic tree based on Taxon id
0
gravatar for Sathish
4.7 years ago by
Sathish50
India
Sathish50 wrote:

Dear all,

I have list of taxon id's collected from NCBI. How to make phylogenetic tree based on taxon id's ?

And also is there any option to create phylogenetic tree for particular plant  (all species included) family?

Kindly recommend programs and reference papers if any.

Thanks in advance.

 

tree taxon id phylogentic ncbi • 2.3k views
ADD COMMENTlink modified 4.7 years ago by David W4.7k • written 4.7 years ago by Sathish50
2
gravatar for David W
4.7 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

PhyloT does this in one click for a set of taxon names or taxon ids.

They use a special syntax for your case of getting all leaves in a larger group:

Euphorbiaceae|subtree

(you can use the dropdown menu to filter species out or only go as low as a given taxonomic rank)

ADD COMMENTlink written 4.7 years ago by David W4.7k
1
gravatar for Pierre Lindenbaum
4.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

I wrote a XSLT stylesheet transforming the output of efetch for taxonomy to graphiz dot: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/taxon2dot.xsl

$ xsltproc taxon2dot.xsl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=9606,9913,30521,562,2157"

digraph G {
n9606[label="Homo sapiens"];
n9606 -> n9605;
n9913[label="Bos taurus"];
n9913 -> n9903;
n30521[label="Bos grunniens"];
n30521 -> n9903;
n562[label="Escherichia coli"];
n562 -> n561;
n2157[label="Archaea"];
n2157 -> n131567;
n131567[label="cellular organisms"];
n2759[label="Eukaryota"];
n2759 -> n131567;
n33154[label="Opisthokonta"];
n33154 -> n2759;
n33208[label="Metazoa"];
n33208 -> n33154;
n6072[label="Eumetazoa"];
n6072 -> n33208;
n33213[label="Bilateria"];
n33213 -> n6072;
n33511[label="Deuterostomia"];
n33511 -> n33213;
n7711[label="Chordata"];
n7711 -> n33511;
n89593[label="Craniata"];
n89593 -> n7711;
n7742[label="Vertebrata"];
n7742 -> n89593;
n7776[label="Gnathostomata"];
n7776 -> n7742;
n117570[label="Teleostomi"];
n117570 -> n7776;
n117571[label="Euteleostomi"];
n117571 -> n117570;
n8287[label="Sarcopterygii"];
n8287 -> n117571;
n1338369[label="Dipnotetrapodomorpha"];
n1338369 -> n8287;
n32523[label="Tetrapoda"];
n32523 -> n1338369;
n32524[label="Amniota"];
n32524 -> n32523;
n40674[label="Mammalia"];
n40674 -> n32524;
n32525[label="Theria"];
n32525 -> n40674;
n9347[label="Eutheria"];
n9347 -> n32525;
n1437010[label="Boreoeutheria"];
n1437010 -> n9347;
n314146[label="Euarchontoglires"];
n314146 -> n1437010;
n9443[label="Primates"];
n9443 -> n314146;
n376913[label="Haplorrhini"];
n376913 -> n9443;
n314293[label="Simiiformes"];
n314293 -> n376913;
n9526[label="Catarrhini"];
n9526 -> n314293;
n314295[label="Hominoidea"];
n314295 -> n9526;
n9604[label="Hominidae"];
n9604 -> n314295;
n207598[label="Homininae"];
n207598 -> n9604;
n9605[label="Homo"];
n9605 -> n207598;
n314145[label="Laurasiatheria"];
n314145 -> n1437010;
n91561[label="Cetartiodactyla"];
n91561 -> n314145;
n9845[label="Ruminantia"];
n9845 -> n91561;
n35500[label="Pecora"];
n35500 -> n9845;
n9895[label="Bovidae"];
n9895 -> n35500;
n27592[label="Bovinae"];
n27592 -> n9895;
n9903[label="Bos"];
n9903 -> n27592;
n2[label="Bacteria"];
n2 -> n131567;
n1224[label="Proteobacteria"];
n1224 -> n2;
n1236[label="Gammaproteobacteria"];
n1236 -> n1224;
n91347[label="Enterobacteriales"];
n91347 -> n1236;
n543[label="Enterobacteriaceae"];
n543 -> n91347;
n561[label="Escherichia"];
n561 -> n543;

after processing with graphviz-dot:

ADD COMMENTlink written 4.7 years ago by Pierre Lindenbaum117k
0
gravatar for bulovic.ana
4.7 years ago by
bulovic.ana70
Croatia
bulovic.ana70 wrote:

What is it exactly that you want to do? In which format would you like your phylogenetic tree to be?

I have written a small script that  enables you to load the entire NCBI taxonomy tree and to query it.

For each of the taxon IDs, you can get the node

a) rank

b) organism name

c) parent node

d) all the children nodes

Additionally, you can find the least common ancestor of a set of nodes and find whether a particular node is a child of some other node.

I can send it to you if that sounds helpful. Is that something that would aid you?

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by bulovic.ana70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1758 users visited in the last hour