GRAMPA: Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis

GRAMPA uses gene tree topologies for inferring the presence and mode of polyploidy in a set of species, placing a whole genome duplication event on a phylogeny, and counting gene duplications and losses in the presence of polyploidy.

Install

Install from bioconda:

You can use conda or mamba to install GRAMPA. The following example uses mamba, but if you prefer conda simply replace "mamba" with "conda" in the command. 

mamba install grampa

After installation, you can run the program with: 

grampa

For other usage instructions and instructions for installing from source, see the README.

Citation

Thomas GWC, Ather SH, Hahn MW. 2017. Gene tree reconciliation with MUL-trees to resolve polyploid analysis. Systematic Biology. 66(6):1007-1018. 10.1093/sysbio/syx044

Identify the mode of polyploidy

GRAMPA may be able to differentiate between the cases of allopolyploidy, autopolyploidy, and no polyploidy.

Place a WGD on a phylogeny

If you know a WGD has taken place on your phylogeny, GRAMPA can place it on the tree.

Count duplications and losses

GRAMPA can accurately count duplications and losses, regardless of the presence of polyploidy.