I understand that many curated trees of life already exist (eg http://tolweb.org/tree/) but is there any website that allows one to input a list of organisms, and then produce the current best guess at their evolutionary relationships?

The best site I managed to find so far is http://itol.embl.de/itol.cgi, which allows you to select specific species from the main tree to plot into a sub-tree, but the tree itself is rather small, so more detailed comparisons cannot be made.

  • $\begingroup$ So you mean a site that can produce a phylogenetic tree for a group of chosen species, based on an underlying database of phylogenetic relationships? $\endgroup$ – fileunderwater Feb 11 '15 at 11:00
  • $\begingroup$ @fileunderwater Yes, that would work. $\endgroup$ – March Ho Feb 11 '15 at 13:49
  • $\begingroup$ I have a similar project, this option you need could be added in the future. Take a look: dao.url.ph/tree/tree.php $\endgroup$ – Rodrigo Feb 11 '15 at 21:53

http://phylot.biobyte.de/ performs the requisite task (generating a phylogenetic tree based on the specific organisms provided, using the NCBI taxonomy tables).

For example, the input of tree elements

Trichomonas vaginalis,Trypanosoma brucei,Homo sapiens,Fibroporia radiculosa,Paramecium tetraurelia,Tetrahymena thermophila,Cryptosporidium muris,Cryptosporidium hominis,Blastocystis hominis

generates the tree

enter image description here

  • $\begingroup$ Really cool resource! $\endgroup$ – fileunderwater Feb 19 '15 at 10:57

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