HIVtree is Bayesian phylogenetic inference program which infers latent integration times of HIV sequences and internal node ages, conditional on a tree topology. It was originally modified from PAML version 4.9 by Ziheng Yang.
To clone the program from GitHub
git clone https://github.com/nage0178/HIVtree.git
To compile the program, navigate to the directory and use the make command.
cd HIVtree/
make
You must have a C compiler, such as gcc or clang, installed to compile the program. To use the make command, you must have the make system installed.
HIVtree is run in the same way as mcmctree. For a full explanation of options and the control file, please see the manual.
./HIVtree control.ctl
Examples are provided in the example directory which includes one example data set with a single gene and another with multiple genes illustrating how to combine inferences across multiple genes.
A recent version of R must be installed with the following packages which are necessary to run the combined analysis.
kdensity
GoFKernel
getopt
Copyright (C) 2022 Anna Nagel
Originally modified from PAML version 4.9 by Ziheng Yang
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.