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PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
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...
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.
Controversial ideas of Williamson, Margulis & others suggest speciation by hybridizing might be more common than originally thought.
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...
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.
treecat is a simple, interactive tool that helps you classify files or database entries into an arbitrary categorytree. Items are automatically classified within a taxonomy quickly and accurately, requiring single key confirmation or correction.