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.

Helpful software:

    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.