• TNRS API
• Tree base API

Improved web service for phylomatic

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

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.

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

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