phyde 0.1.0

Hybridization detection using phylogenetic invariants

HyDe: hybridization detection using phylogenetic invariants

Read the Docs

Installation

Requirements:

• Python 2.7

• Cython

• Numpy

• Scipy

• Pandas

• Matplotlib

• Seaborn

• C++ compiler (g++ >= v4.8 preferred)

HyDe is a Python package that wraps a primary C++ program for running a hybridization detection analysis. We have provided a Makefile that will compile the C++ executable (hyde_cpp) and will then install the HyDe 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 HyDe Python package
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 hyde 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)