Update AdapterRemoval to 1.3-GG2 (pre 1.4).
Make stdout a property.
Make concatenate_input_bams a public function.
Add AtomicCmd.wait function.
Add depth histogram node, based on BedTools coverageBed.
Adding depth histogram to bam_pipeline.
Convert tabs to spaces.
Enable, and fix, a few warnings.
Fix for EXAML model check.
Add MPI wrapper for AtomicParams.
Default to non-verbose, allow disabling of tree-collapsing.
Add RAxMLBootstrapNode, for generating Phy files.
Add multithreading to EXaMLNode.
Fix ParsimonatorNode description.
Fix case of key in makefile.
Initial PAML support.
Initial EXaML support.