A mixture of scripts and libraries to help with sequence data manipulation, tree parsing, and other things.
These scripts can be used for many tasks including sequence handling, tree making, and sequence alignment. Some of these programs are mainly used as wrappers to easily run other genomics or phylogenetics programs on a bunch of files.
| Directory | Description |
|---|---|
| legacy/ | Previous versions of scripts and libraries as well as defunct scripts and libraries that are no longer maintained. |
| python/ | Standalone Python scripts and libraries with functions pertaining to running genomics programs, sequence handling, and tree manipulation. Also contains scripts to generate commands for many files from some common programs and an associated SLURM submission script. |
| r/ | Standalone R scripts for tree manipulation and figure design. |
| utils/ | Various other tools as shell scripts. |