hyphy command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

hyphy: command not found

or when using sudo you get the following error message

sudo: hyphy: command not found

Solutions to hyphy: command not found

How To Fix hyphy: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu hyphy is provided by hyphy-pt package.

hyphy-pt is:

HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.

This package provides an executable using pthreads to do multiprocessing.

To fix this problem, we can install more using the command below.

sudo apt-get -y install hyphy-pt

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install hyphy-pt.

sudo apt -y install hyphy-pt

Or if you have aptitude installed you can use the following command.

sudo aptitude install hyphy-pt

Summary

In this tutorial we learn how to fix hyphy command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.