5. More info

Recommended reading

• Unix shell background info here, here, here, and here.
• GNU Bash Reference Manual

Developer information

TODO

• Improve option and usage sections of BEASTRunner.sh script. DONE! ✅
• Add MrBayes scripts DONE! ✅
• Add options to MrBayesPostProc script, e.g. for burnin frac and stepping-stone MLE analysis. DONE! ✅
• Change new phylipSubsampler script so that it accounts for missing data (currently does not).
• Give supercomputer scripts options (header w/flags) that will work for both a) TORQUE/PBS and b) SLURM Workload Manager cluster management and job scheduling systems (need meticulous work on this in Super-pyRAD2PartitionFinder.sh, BEASTRunner.sh, BEASTPostProc.sh, and RAxMLRunner.sh)
• Add mrbayes and beast model options to pyrad2PartitionFinder.sh and supercomputer version of the same script.
• Make pyrad and ipyrad batch run scripts available
• Consider separate scripts to work with ipyrad
• Add capacity of adding or not adding path sampling/stepping-stone sampling to BEAST runs (use BEASTRunner.sh as springboard to develop tools in BEAST_PathSampling dir)

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