Phylomatic

A database for applied phylogenetics (details here)

NEWS! [9 Jun 2007] 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.
Several tools are available to construct a taxonomy consistent with phylomatic:
- A checker against the master tree in phylomatic [CRITICAL].
- A lookup of genus names against a list at Kew, and the APweb family list (used in the master tree).
- A lookup of family names against the APweb family list (used in the master tree).
- A fuzzy lookup of genus names against a list at Kew.

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 (pseudo) branch lengths (in My)

No
Yes (obtained by running `phylocom bladj' on the megatree with ages from Wikstrom et al. (2001)

4. Choose the master phylogeny to use

Maximally resolved seed plant tree. Please read about tree support and limitations.
Conservative 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: (Newick)
User-supplied tree as URL:

5. Phylogenize!

Partially funded by DEB-0212873

Last revised: $Date: 2007/06/09 15:26:40 $