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delimtools — License

R package

Copyright (C) 2023–2026 Pedro S. Bittencourt, Rupert A. Collins, Tomas Hrbek

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

A copy of the GNU Affero General Public License is available at https://www.gnu.org/licenses/agpl-3.0.html.

Bundled third-party components

delimtools embeds compiled C code from several independent projects. Each component retains its original copyright and license; their terms are reproduced below.

mPTP — multi-rate Poisson Tree Processes

Files: src/mptp/

Copyright (C) 2015 Tomas Flouri, Sarah Lutteropp

Licensed under the GNU Affero General Public License, version 3 or later (AGPL-3+). Full text: https://www.gnu.org/licenses/agpl-3.0.html

Contact: Tomas Flouri Tomas.Flouri@h-its.org
Heidelberg Institute for Theoretical Studies
Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany

ABGD — Automatic Barcode Gap Discovery

Files: src/abgd/

Copyright (C) 2008–2013 Guillaume Achaz

Licensed under the GNU Lesser General Public License, version 2.1 or later (LGPL-2.1+). Full text: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html

Contact: Guillaume Achaz achaz@abi.snv.jussieu.fr

ASAP — Assemble Species by Automatic Partitions

Files: src/asap/

Copyright (C) 2015–2016 Guillaume Achaz, Sophie Brouillet

Licensed under the GNU Lesser General Public License, version 2.1 or later (LGPL-2.1+). Full text: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html

Contact: Guillaume Achaz guillaume.achaz@mnhn.fr

GMYC — General Mixed Yule-Coalescent

Files: src/gmyc/

The C engine in src/gmyc/ is a translation of the gmyc.R implementation distributed in the splits R package (Fujisawa & Barraclough 2013).

Copyright (C) 2013 Tomochika Fujisawa, Timothy G. Barraclough

Licensed under the GNU General Public License, version 2 or later (GPL-2+). Full text: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html

bGMYC — Bayesian General Mixed Yule-Coalescent

The Bayesian GMYC sampler (R/bgmyc.R, src/gmyc/gmyc_r.c) is derived from the bGMYC R package (Reid & Carstens 2012).

Copyright (C) 2012 Noah M. Reid, Bryan C. Carstens

Licensed under the GNU General Public License, version 3 or later (GPL-3+). Full text: https://www.gnu.org/licenses/gpl-3.0.html