phyde 0.1.1

Hybridization detection using phylogenetic invariants

HyDe: hybridization detection using phylogenetic invariants

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Installation

Requirements:

• Python 2.7

• Cython

• Numpy

• Scipy

• Pandas

• Matplotlib

• Seaborn

• C++ compiler (g++ >= v4.8)

HyDe is a software package that detects a signal for hybridization in phylogenomic data sets using phylogenetic invariants. The primary interface for HyDe is a Python module called phyde (Pythonic Hybridization Detection). phyde provides a suite of tools for performing hypothesis tests on triples of taxa to detect hybridization. It also has built in functions to wrap calls to the pure C++ version of HyDe, hyde_cpp. We have provided a Makefile that will compile the hyde_cpp C++ executable and will then install the phyde Python package using the setup.py file. To ensure that the necessary dependencies are available, we suggest using a Python distribution such as Miniconda.

# To install dependencies
pip install cython numpy scipy pandas matplotlib seaborn

# Clone HyDe repository from GitHub
git clone https://github.com/pblischak/HyDe.git
cd HyDe

# Compile hyde_cpp using `make`
make

# Now install phyde module
python setup.py install

# Test the installation
make test

Running HyDe from the Command Line

Type run_hyde.py -h for options.

run_hyde.py -i <infile> -m <map-file> -o <outgroup> \
            -n <num-ind> -t <num-taxa> -s <num-sites> \
            --prefix <prefix>

Running HyDe in Python

import phyde as hd

# Run a hyde analysis
hd.run_hyde(...)

# import a data set for testing particular triples
data = hd.HydeData("data.txt", "map.txt", "out", 16, 4, 250000)