camwebb / phylomatic-ws

Improved web service for phylomatic

phylomatic-ws

IMPORTANT: as of mid-2022, the phylodiversity.net website, and the online phylomatic, is NOT UNDER MY CONTROL. An unknown person has (legitimately) bought the phylodiversity.net domain, and is illegitimately hosting old, depreciate web pages at the site. There is nothing I can do to fix this.

Links

• TNRS API
• Tree base API

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