Phylomatic

 details
phylocom
webb
donoghue

An online tool to assemble species lists into phylogenies

(original details here)

2009-11-10 changes

The base tree for online phylomatic is now a APG3 derived megatree. The base tree used for the past couple years had not been updated, and it is time to sync the online phylomatic with the phylomatic2 database. However, this requires users adopting some changes: i) I have restricted some of the options available on this page, ii) The major change is that the phylomatic2 database uses all lowercase names for taxa in the database, and so your input trees must be all lowercase (for taxa to be matched; the terminal name can still contain uppercase chars). A good editor will be able to `downcase’ your input file in a single action. I apologize for this step if you have got used to using this resource as is, but for a while I have been urging users to switch to the desktop phylomatic (included in phylocom) and the phylomatic2 database. At least you will be able to access an up-to-date tree this way. Note that the Davies tree still uses uppercase first characters of taxon names.

API

Added a XML output option, and the ability to send requests as GET statements, so phylomatic can be used as a simple web service now.

1. Paste your community list

  • Format (simple): Family/Genus/Genus_species RET
  • A sample community is available to play with.
  • This `/’ delimited format allows the creation of unlimited user-defined structure (see sample). The program reads the string from right to left, matching the taxon at the first position it can in i) the growing user-defined tree, or ii) the `megatree.’
  • No empty lines, and check the RETURN after the last character.

2. Choose output format

Newick (including diagnostics)
XML (phylomatic meta data format)
Nexus
Graphical output (JPG) – using drawgram from PHYLIP (v3.6). And then ghostscript.

3. Choose the master phylogeny to use

Maximally resolved seed plant tree. Please read about tree support and limitations.
Angiosperm consensus tree from Davies et al. (2004) (Thanks, Jonathan!). See here for info.
User-supplied tree as URL:

4. Phylogenize!



Partially funded by DEB-0212873