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 with bioconda: 

conda install -c bioconda grampa

Otherwise, just download the program straight from github by clicking the download button below. The program is just a python script with no other dependencies, so it should work out of the box!

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.