phacts 1.8

A program to predict the lifestyle (virulent/lytic or temperate/lysogenic) of a phage genome

PHACTS

A simple program to classify the lifestyle of phages.

Introduction

Phage Classification Tool Set (PHACTS) utilizes a novel similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The similarity algorithm creates a training set from phages with known lifestyles and along with the lifestyle annotation, trains a Random Forest to classify the lifestyle of a phage. PHACTS predictions are shown to have a 99% precision rate.

To install PHACTS,

pip install phacts

or

 git clone https://github.com/deprekate/PHACTS.git
 pip install PHACTS/ --user

This is the new python based recoding of my original perl code, and is in an alpha state for now.

• I have included fasta35 binaries for Linux and OSX, that should install automatically. For Windows, you will need to download a windows fasta35 binary, and make it visible on the PATH

I have tried to replicate exactly the functionality of the original published version.

PHACTS Example

Run on included sample data, the output is the predicted lifestyle and the class probabilities:

$ phacts.py tests/NC_001416.faa 
Class       probability  standard deviation
Temperate   0.626273726  0.101584648