Improved web service for phylomatic
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pmws

README.md

phylomatic-ws

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Improved web service for phylomatic

Internal phylogeny representation

Each node is represented by the following array values:

  • nodename : the node identifier (string)
  • parent[nodename] : the parent node identifier
  • bl[nodename] : branch length to the parent node (float or string)
  • taxon[nodename] : the taxon assoc with that node identifier (string)
  • nDaughter[nodename] : the number of distal edges (integer)
  • note : any notes associated with the node (string)
  • lDaughter[nodename] : the left daughter of a node, created only during writing of newick (string)
  • rSister[nodename] : the right sister of a node, created only during writing of newick (string)
  • age[nodename] : the age of the node, measured from (ultramentric) tips (integer or float)

Other globals valiables:

  • hasBL : does the tree contain BLs? (0|1)
  • totalBL : the total tip to root BL sum (assumes an ultrametric tree) (float or string)
  • root : the root node

Performance

Matching 10 taxa in the Smith 2011 megatree:

  $ cat eg/input1 | /usr/bin/time pmws

See it live:

  http://phylodiversity.net/phylomatic/pmws?storedtree=smith2011
    &informat=newick&method=phylomatic&taxa=Bicuiba_oleifera%0AGu
	atteria_dolichopoda%0AIteadaphne_caudata%0AGonocarpus_leptoth
	ecus%0AAmylotheca_subumbellata%0AImpatiens_davidi%0ACalochort
	us_argillosus%0ALilium_lankongense%0AGagea_sarmentosa%0ACepha
	lanthera_rubra&outformat=newick&clean=true

Does the match in 1.8 seconds on my quad-core Intel i5 laptop.

Data input examples

Here are some possible input URIs:

“Select seal,sea_lion,monkey from a NeXML tree at the PhylotasticTreeStore” (RUN):

  http://phylodiversity.net/phylomatic/pmws?treeuri=http%3A%2F%2F
    phylotastic.nescent.org%2FPhylotasticTreeStore%2Fphylows%2Ftre
	e%3Ftree%5Furi%3Dhttp%253A%252F%252Fphylotastic.nescent.org%25
	2Ftrees%252FTreemytree5&informat=nexml&method=phylomatic&taxa=
	seal%0Asea_lion%0Amonkey&outformat=newick&clean=true

“Convert a CDAO phylogeny to Newick” (RUN):

  http://phylodiversity.net/phylomatic/pmws?treeuri=http://phylo
    diversity.net/phylomatic/eg/tree1.cdao.rdf&informat=cdaordf&
	method=convert&outformat=newick

To Do

  • Send/receive compression with gzip
  • Graft in whole trees
  • More ouput formats
  • Add jsPhyloSVG viewer