naturalis/supersmart repository overview

⁠INFO

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.

⁠INSTALLATION

Installation depends on vagrant and Virtualbox, see INSTALL.md, the installation guide on the wiki page⁠ and the project website⁠.

⁠COMMANDS

The functionality of the pipeline is exposed via the smrt⁠ command. The 'smrt' command offers twelve subcommands⁠, representing each step of the pipeline.

⁠CONFIGURATION

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.

⁠EXAMPLES

The examples/* directories contain instructional examples to demonstrate the input file formats.

⁠BUILD STATUS

Currently, the build status at Travis is: