# mrbayes_volpiano

This is a fork of MrBayes v3.2.7a, a programme for estimation of phylogenetic trees using Bayesian inference. This fork differs from the original in that the standard character coding is no longer intended for morphology in biological datasets but rather for the encoding of plainchant melodies in the volpiano format. The original README is provided below as well as the license and modified source code. A note has been added to the greeting text to make it clear that this is a fork only intended to be used for analysing plainchant melodies in volpiano format rather than the original biological sequence data.

If you use this programme please cite both the original paper (and the appropriate sections in the command `citations`):

Ronquist, F. et al. 2012. MRBAYES 3.2: Efficient Bayesian phylogenetic     
         inference and model selection across a large model space.               
         Syst. Biol. 61:539-542.
	 
and the paper in which we present the application to this new study system:

Hajič jr., J., *Ballen, G.A.*, Mühlová, K.H., & Vlhová-Wörner, H. (2023). Towards Building a Phylogeny of Gregorian Chant Melodies. Proceedings of the 24th International Society for Music Information Retrieval Conference, 571–578. [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10340442.svg)](https://doi.org/10.5281/zenodo.10340442)

Gustavo A. Ballen, PhD.

============ Original README

Hi,

This is the GitHub repository for MrBayes, a program used for Bayesian
inference of phylogeny.


Build instructions, very very short version (would install MrBayes as
"/usr/local/bin/mb" on a Unix system):

    git clone --depth=1 https://github.com/NBISweden/MrBayes.git
    cd MrBayes
    ./configure
    make && sudo make install

    Refer to the document called "INSTALL" for further information.


Current repository directory layout:

    .
    ├── am-*           : Files relating to the build system
    ├── doc
    │   ├── manual     : The manual
    │   └── tutorial   : A tutorial
    ├── examples       : Example input data sets
    └── src            : C source code


The web site is available at

    http://NBISweden.github.io/MrBayes/


Historical releases are tagged with "v3.2.0" (etc.) from release 3.2.0
onwards.

The 'master' branch contains releases.

The 'develop' branch should hopefully, at all times, contain working
development code that at least compiles.  Apart from simple fixes, new
development happens on feature branches off the 'develop' branch, and
are merged back into 'develop' when finished.  This more or less follows
the "git-flow" branching model.

The 'gh-pages' branch contains the web site (only).

The 'testing' branch contains testing data files (only).

After release 3.2.6 (November 2015), MrBayes entered "maintenance mode",
and its care has been passed over to NBIS (National Bioinformatics
Infrastructure Sweden, http://nbis.se/).  The original development
team is still involved with the program, but any future releases will
probably be geared more towards bug-fixes rather than addition of new
features.

With kind regards,
    Andreas (Kusalananda) Kähäri, and
    Johan Nylander
    NBIS