This is the source code repository of the Self-Updating Platform for the Estimation of Rates of Speciation, Migration, And Relationships of Taxa (SUPERSMART), a pipeline for estimating time-calibrated species trees from public data. Constantly updated information about the pipeline can be retrieved from the project website at www.supersmart-project.org. An article about SUPERSMART has been published in the journal Systematic Biology.
Installation depends on vagrant and Virtualbox, see INSTALL.md, the installation guide on the wiki page and the project website.
The functionality of the pipeline is exposed via the smrt command. The 'smrt' command offers twelve subcommands, representing each step of the pipeline.
Basic configuration is done via options passed to the 'smrt' command. Advanced configuration of the pipeline API is possible in the conf/supersmart.ini file. The smrt-config command provides an interface for changing the configuration file.
The examples/* directories contain instructional examples to demonstrate the input file formats.
Currently, the build status at Travis is: