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updated README with manuscript details
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# Species Delimitation
# Species delimitation using the multi-rate Poisson Tree Processes (mPTP)

[![License](https://img.shields.io/badge/license-AGPL-blue.svg)](http://www.gnu.org/licenses/agpl-3.0.en.html)
[![Build Status](https://travis-ci.org/Pas-Kapli/mptp.svg?branch=master)](https://travis-ci.com/Pas-Kapli/mptp)
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to the mptp man page `man/mptp.1` in a folder included in your `$MANPATH`. The
PDF version of the manual is available in `doc/mptp_manual.pdf`.

## Implementation details and method description

Please see the manuscript for details:

Kapli T, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. (2016) Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11):1630-1638. doi:[10.1093/bioinformatics/btx025](https://doi.org/10.1093/bioinformatics/btx025)




## Command-line options
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## Code

File | Description
--------------------|----------------
**arch.c** | Architecture specific code (Mac/Linux).
**auto.c** | Code for auto-detecting minimum branch length.
**aic.c** | Code for Bayesian Single- and multi-rate PTP.
**mptp.c** | Main file handling command-line parameters and executing corresponding parts.
**mptp.h** | MPTP Header file.
**dp.c** | Single- and multi-rate DP heuristics for solving the PTP problem.
**fasta.c** | Code for reading FASTA files.
**lex_rtree.l** | Lexical analyzer parsing newick rooted trees.
**lex_utree.l** | Lexical analyzer parsing newick unrooted trees.
**likelihood.c** | Likelihood rated functions.
**Makefile.am** | Automake file for generating Makefile.in.
**maps.c** | Character mapping arrays for converting sequences to the internal representation.
**multirun.c** | Functions to execute multiple MCMC runs and compute ASD of support values.
**output.c** | Output related files.
**parse_rtree.y** | Functions for parsing rooted trees in newick format.
**parse_utree.y** | Functions for parsing unrooted trees in newick format.
**random.c** | Functions for creating a random delimitation.
**rtree.c** | Rooted tree manipulation functions.
**svg.c** | SVG visualization of delimited tree.
**svg_landscape.c** | SVG visualization of likelihood landscape.
**util.c** | Various common utility functions.
**utree.c** | Unrooted tree manipulation functions.
| File | Description |
| --------------------| --------------------------------------------------------------------------------- |
| **arch.c** | Architecture specific code (Mac/Linux). |
| **auto.c** | Code for auto-detecting minimum branch length. |
| **aic.c** | Code for Bayesian Single- and multi-rate PTP. |
| **mptp.c** | Main file handling command-line parameters and executing corresponding parts. |
| **mptp.h** | MPTP Header file. |
| **dp.c** | Single- and multi-rate DP heuristics for solving the PTP problem. |
| **fasta.c** | Code for reading FASTA files. |
| **lex_rtree.l** | Lexical analyzer parsing newick rooted trees. |
| **lex_utree.l** | Lexical analyzer parsing newick unrooted trees. |
| **likelihood.c** | Likelihood rated functions. |
| **Makefile.am** | Automake file for generating Makefile.in. |
| **maps.c** | Character mapping arrays for converting sequences to the internal representation. |
| **multirun.c** | Functions to execute multiple MCMC runs and compute ASD of support values. |
| **output.c** | Output related files. |
| **parse_rtree.y** | Functions for parsing rooted trees in newick format. |
| **parse_utree.y** | Functions for parsing unrooted trees in newick format. |
| **random.c** | Functions for creating a random delimitation. |
| **rtree.c** | Rooted tree manipulation functions. |
| **svg.c** | SVG visualization of delimited tree. |
| **svg_landscape.c** | SVG visualization of likelihood landscape. |
| **util.c** | Various common utility functions. |
| **utree.c** | Unrooted tree manipulation functions. |

## The team

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* Alexandros Stamatakis
* Tomáš Flouri

## Citing mPTP

Please cite the following publication if you use mPTP:

Kapli T, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. (2016) Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11):1630-1638. doi:[10.1093/bioinformatics/btx025](https://doi.org/10.1093/bioinformatics/btx025)

# References

* Zhang J., Kapli P., Pavlidis P., Stamatakis A. (2013)
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