SuperTreeBASE - data dump and code to summarize TreeBASE

This repository contains a nearly complete dump of the contents of TreeBASE, the database of phylogenetic knowledge. In addition there are various scripts and (make-based) pipelines to summarize the dump in various ways, including:

• topologically, by integrating the tree topologies in the database into MRP matrices that can be analyzed
• taxonomically, by summarizing coverage of classes and by visualizing taxonomic overlap between studies
• chronologically, by summarizing the growth in character data of various types over time

Licensing

All data made available here are reproduced from TreeBASE and the NCBI taxonomy. As such, the terms of the original rights holders apply (which are very lenient: if you want to do science with what's here, feel free to do so). The source code is open source and made available under an MIT license.

Structure

• TreeBASE data are in data/treebase, in NeXML format
• taxonomy data are in data/taxdmp, in NCBI dmp format
• metadata/* contains summaries computed from the data
• script/* contains source code organized in pipelines

Pipelines

All pipelines in the subfolders of script/ are executed by running make targets defined in the Makefiles. The targets invoke Perl scripts in the same folder. To find out which targets to run and which dependencies to resolve you will have to study the source code.

• characters - computes usage of different types of character data over time
• circos - creates data tracks and links for input into Circos
• cliques - creates a GraphViz network of taxonomic links between studies
• supertree - creates MRP matrices for analysis
• test - contains throwaway scripts that can be ignored