Phylomatic

 details
phylocom
webb
donoghue

A database for applied phylogenetics (details here)

NEW! Standalone Phylomatic included in Phylocom 3.34b
Fast, handles large trees, transfers branch length data to user tree!

1. Paste your community list

  • Format: Family TAB Genus TAB species TAB code (optional) RET
  • Spaces can also be used to separate columns (but not spaces and tabs). No empty lines.
  • 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.
  • A sample community is available to play with.

2. Choose type terminal name in output

“Genus_species” (no codes needed in 4th column)
code (in 4th column)

3. Choose output format

Graphical output (BMP) – using drawgram from PHYLIP (v3.6). Thanks to Joe Felsenstein!
Newick
Nexus
Node-as-factor (space-delimited; for contrast tests)
Newick with interior node names
Newick with nodes numbered
Nexus with nodes numbered

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, with family node names, = “-aceae”)
User-supplied tree as URL:

5. Choose the return method

Returned to browser
Waiting page (Only if a large job is causing the browser to time-out; will be overwritten on next phylomatic use).

6. Phylogenize!


NOTE: the server processor is slow. Please be patient (up to 30 seconds)!

Then save result to a text file, and display with a tree drawing program (e.g. DRAWGRAM in PHYLIP). The Nexus file opens in MacClade and PAUP. Tip: to add branch lengths of 1.0 to all branches in a Newick file, replace (with an editor, e.g. BBEdit) ‘,’ with ‘:1.0,’, and ‘)’ with ‘:1.0)’. The adjusted tree will open in TreeEdit.



Partially funded by DEB-0212873

Last revised: $Date: 2005/01/06 01:18:11 $