Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
JavaScript Perl Other
Clone or download
Pull request Compare This branch is 2023 commits ahead of rvosa:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
conf
data
examples
lib/Bio
script
sql
t
web
.gitattributes
.gitignore
.travis.yml
INSTALL.md
LICENSE
MANIFEST.skip
Makefile.PL
README.md

README.md

Build Status

SUPERSMART

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. An article about SUPERSMART has been published in the journal Systematic Biology.

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:

Build Status