Michael G. Campana, 2019
Smithsonian Conservation Biology Institute
Pipeline script to generate input files for ASTRAL and SVDquartets + PAUP* from a collection of phyluce UCE loci alignments in nexus format.
The software is made available under the Smithsonian Institution terms of use.
In the terminal:
git clone https://github.com/campanam/uce2speciestree
cd uce2speciestree; chmod +x uce2speciestree.rb
This pipeline is hard-coded for the Smithsonian High Performance Computing Cluster ('Hydra') using SGE. It requires RAxML and Ruby and loads those software as modules. The code will not work on other clusters without manual editing of the script. Assuming a similarly configured SGE cluster, the modules and executables to be changed are located in the write_array_qsub method. The software is provided 'as-is' as a useful reference, but there are no current plans to develop it for general use.
ruby uce2speciestree.rb will show the help menu for execution.
Campana, M.G. 2019. uce2speciestree. https://github.com/campanam/uce2speciestree.