GRAMPA is a program to identify and place polyploidy events on a phylogeny and count duplications and losses in the presence of polyploidy.
What follows is a brief explanation of the options. Please see the project website for much more in depth info about the algorithm and examples of the program's usage.
Thomas GWC, Ather SH, Hahn MW. 2017. Gene-tree reconciliation with MUL-trees to resolve polyploid events. Systematic Biology. 66(6):1007-1018. https://doi.org/10.1093/sysbio/syx044
Change log:
- Re-factor of much of the code that handles inputs and outputs.
- Reformatted output files to be easier to handle when post-processing (see the website README for more info).
- Removed
-din favor of--st-onlyand--no-st
Version 1.3 (February 14, 2020): Added the --numtrees and --version options. Dropped support for Python 2.
Version 1.2 (April 16, 2017): Added the -p option so users can specify the number of processes GRAMPA should utilize.
Simply download the program and run it. You may want to add the GRAMPA folder to your $PATH variable for ease of use.
GRAMPA is also available through bioconda. Thanks to nathanweeks for setting that up!
The first thing you should do when you try to run GRAMPA is make sure everything is working with some test files. You can do this easily by running the --tests command:
python grampa.py --tests
If all tests pass, then you're good to go! Basic usage in a real case would be:
python grampa.py -s [species tree file] -g [gene trees file] -o [output directory]
This would perform a full search for the optimal (lowest-scoring) MUL-tree on the input species tree. The other important options are -h1 and -h2. Read more about them below and on the project website.
| Option | Description |
|---|---|
| -s | A file or string containing a bifurcating, rooted species tree in Newick format. This tree can either be singly-labeled or MUL. |
| -g | A file containing one or more bifurcating, rooted, Newick formatted gene trees. Gene trees with polytomies will be removed from the dataset. |
| -h1 | A space separated list of nodes to search as the polyploid clade. Cannot be used with used with --multree. If nothing is entered all nodes will be considered. |
| -h2 | A space separated list of nodes to search as possible parental lineages for all nodes specified with -h1. Cannot be used with used with --multree. If nothing is entered all possible nodes for the current h1 will be considered. |
| -c | The maximum number of initial groups to consider for any gene tree. Default: 8, Max value: 18 |
| -o | Output directory name. If the directory is not present, GRAMPA will created it for you. |
| -f | By default, all output files created by GRAMPA will have the prefix 'grampa'. You can specify a different prefix with this option. |
| -v | Control the amount of output printed to the screen. 0: print nothing. 1: print only some info at the start. 2: print all log info to screen. 3 (default): print all log info to the screen as well as progress updates for certain steps. |
| -p | The number of processes GRAMPA should use. |
| --multree | Set this flag if your input species tree is a MUL-tree. |
| --labeltree | The program will simply label your input species tree. |
| --numtrees | The program will simply count the number of possible MUL-trees given -s. -h1, and -h2 may also be supplied. |
| --buildmultrees | Build MUL-trees given -s, -h1 and -h2. |
| --checknums | If this flag is entered, the program will just calculate the number of groups per gene tree and exit. No reconciliations will be done. |
| --st-only | Only perform reconciliations to the singly-labeled tree input with -s. |
| --no-st | Skip performing reconciliations to the singly-labeled tree input with -s and only do reconciliations to MUL-trees. |
| --maps | Output the node maps for each reconciliation in addition to the scores. The maps will be placed in the detailed output file. |
| --version | Print out version info and exit. |
| --tests | Run the tests script. |