New upstream version 0.2.3

All notable changes to `mptp` will be documented in this file.

This project adheres to [Semantic Versioning](http://semver.org/).

## [0.2.3] - 2017-07-25

### Fixed

 - Replaced hsearch which was causing problems on APPLE with custom hashtable

 - Corrected file name in error messages when failing to open files

## [0.2.2] - 2017-01-31

### Fixed

 - Regular expressions now allow scientific notation when parsing branch lengths

# 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)

[![Build Status](https://travis-ci.org/Pas-Kapli/mptp.svg?branch=master)](https://travis-ci.org/Pas-Kapli/mptp)

## Introduction

using the command

```bash

sudo apt-get install libgsl0-dev flex bison autotools-dev

sudo apt-get install libgsl0-dev flex bison autotools-dev autoconf

```

Optionally, you can install the bash auto-completion for mptp. To do that,

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

## 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

* 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)

# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])

AC_INIT([mptp], [0.2.2], [Tomas.Flouri@h-its.org])

AC_INIT([mptp], [0.2.3], [Tomas.Flouri@h-its.org])

AM_INIT_AUTOMAKE([subdir-objects])

AC_LANG([C])

AC_CONFIG_SRCDIR([src/mptp.c])

parsing trees.  Improved the accuracy of ASV score by also taking into account

tips forming coalescent roots.  Fixed memory leaks that occur when parsing

incorrectly formatted trees.

.TP

.BR v0.2.3\~ "released July 25th, 2017"

Replaced hsearch() with custom hashtable. Fixed minor output error messages.

.RE

.LP

svg.c \

svg_landscape.c \

util.c \

utree.c

utree.c \

hash.c \

list.c