itaxotools-fitchi 1.3.0

Haplotype genealogies based on Fitch distances

Fitchi

Haplotype genealogies based on Fitch distances.

This is a Python package for Fitchi. For more information on the original, see here.

Click for a comprehensive output example

Installation

Fitchi is available on PyPI. You can install it through pip:

pip install itaxotools-fitchi

Usage

The original command-line tool is included as part of the installation. It produces HTML files from Nexus files, as demonstrated with the example input and output files. For information about the available options, you may refer to the original documentation.

Note that you will need all dependencies in order to run Fitchi this way:

fitchi examples/example.nex examples/example.html -m 3 -p pop1 pop2
start examples/example.html  # browse results on Windows

You may also invoke Fitchi from Python using compute_fitchi_tree(). This returns a tree in the form of HaploNode objects, which can be used for downstream analysis or visualization. Only scipy is required in this case.

See the scripts folder for some usage examples.

Dependencies

Fitchi requires scipy. Extra statistics require biopython. Visualization requires pygraphviz.

To install pygraphviz, please follow these instructions from the pygraphviz documentation. For example, to install pygraphviz on Windows, first install Graphviz to the default location, then execute the following command in PowerShell:

pip install pygraphviz --config-setting build_ext^="^--include-dir=C:\Program Files\Graphviz\include" --config-setting build_ext^="^--library-dir=C:\Program Files\Graphviz\lib"

Citation

Matschiner M (2015) Fitchi: Haplotype genealogy graphs based on the Fitch algorithm. Bioinformatics, 32:1250-252.