People and places related to GRAMPA:
Gregg Thomas / The lead developer of GRAMPA
Hahn lab / GRAMPA was developed in Matthew Hahn's lab at Indiana University
GRAMPA github / GRAMPA's github repository.
MUSCLE / Fast alignment software for DNA or amino acid sequences.
RAxML / Maximum likelihood software for making gene trees from DNA or amino acid alignments.
ASTRAL / Coalescent based software for making species trees from gene trees.
Notung / Another reconciliation program with lots of nice functions. Can be used to root gene trees based on a DupLoss model and for bootstrap rearrangement.
FigTree / Software for rendering phylogenetic trees. All trees in the Examples and Results sections were rendered in FigTree and edited with Adobe Illustrator.
SeaView / A versatile program for quick viewing of alignments and phylogenetic trees
JPrIME / Software used to simulate gene trees with varying rates of gene gain and loss.
Previous versions of GRAMPA
Versions after these are located in the github repo.
Version 1.1 / March 22, 2016 / Implemented gene tree filtering and several useful options. No parallelization.
Version 1.0 / Summer 2015 / The first release. No gene tree filtering.