ClonalFrameML command not found

Introduction

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

ClonalFrameML: command not found

or when using sudo you get the following error message

sudo: ClonalFrameML: command not found

Solutions to ClonalFrameML: command not found

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

In Ubuntu ClonalFrameML is provided by clonalframeml package.

clonalframeml is:

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by Xavier Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny.

ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame which was previously described by Didelot and Falush (2007). The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues

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

sudo apt-get -y install clonalframeml

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

You can also use apt command to install clonalframeml.

sudo apt -y install clonalframeml

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

sudo aptitude install clonalframeml

Summary

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