phyinc 1.0

Make sequence logos using Felsenstain's phylogenetically independent contrast metod to take evolution into account

Phylogenetically Independent Contrasts Logo

Description

PhyInC Logo (pronounced Fink Logo) for short is a tool to take .fa and .tree files to create a phylogenetically conditioned sequence logo, using Felsensteins Phylogenetic Independent Contrast.

Install from PyPI.org

pip3 install phyinc

It is always a good idea to use virtual environments, see below.

Install from a downloaded GitHub repository

For dependencies, start a virtual env as good practice:

> python3 -m venv .
> source venv/bin/activate
> pip3 install biopython weblogo matplotlib numpy

If you are on mac

> brew install ghostscript

To install the current package:

> pip3 install .

Examples

Run this command:

> phyinc ./examples/synthetic_data/ex1_t1.tree ./examples/synthetic_data/ex1.fa

This should create a PDF named "ex1.fa_seqlogo.pdf" in the examples folder.

Files Inside

README.md src/ |-- phyinc/ |-- config.py
|-- phyinc.py / |-- io.py |-- version.py examples/ |-- ex1_t1.tree |-- ex1.fa

config.py is a configuration file used to save the confirguration from phyinc

ex1_t1.tree is a .tree file provided as an example

ex1.fa is a .fa file provided as an example

phyinc.py is the program

Regular_logo.pdf is the output if you run the program on the example files provided

With_PIC_logo.png is the output if you run the program on the example files provided

License

GPLv3

Authors

• Haolin Guo wrote the basic code as part of his BSc project.
• Kyle Tenn helped make the code into a Python/PyPI package.
• Lars Arvestad oversaw and helped with creating the final Python/PyPI package.