Phylogentic tree based on Taxon id

Question

[Sathish]

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.

Answer 1

[Pierre Lindenbaum]

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:

Answer 2

[David W]

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)

Answer 3

[bulovic.ana]

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?