Search Results for "tree"

PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade-defining polymorphism. This functionality has been implemented using the tabix tool on the server side, providing simple and rapid access to the information at each tree node, including informative SNPs stored in VCF-similar files. ...

lib_data_io is a set of PHP libraries designed to easily move complex sets of data between PHP array data structures and a variety of sources and destinations including JSON, XML, ICAL, MySQL, HTML, Trac WIKI, text, LDIF, and plot images.

The SplitDB project gives practitioners of statistical tools for inferring phylogenies a way to store, retrieve and visualize important properties, like convergence, of the overwhelmingly large resulting tree-sets produced by these tools.

...Taking this concept to the nth degree & assuming that indeed, speciation mostly occurs by hybridizing events, not the accumulation of mutations or genetic drift, here is a catalogueoflife2gedcom converter. It allows the tree of life to be displayed as a human genealogy tree with hybridizing events depicted as "marriages." The idea then is that mutation accrual & genetic drift are the determining factors for "species maturation," not speciation itself. Unfortunately the Catalogue of Life Project, catalogueoflife.org, changed its database format more recently, so this converter only works on older versions of the data. ...

A PHP webapp to upload taxonomic checklists as Excel or CSV files to be served as TDWG TCS XML/RDF. It can handle multiple checklists, has a Tapir light webservice and a taxonomic tree of species names created from taxonomy in a checklist can be browsed.

A basic implementation of an AVL Tree in PHP 5.