How To Install clonalframeml on Debian 10

Learn how to install clonalframeml on Debian 10 with this tutorial. clonalframeml is Efficient Inference of Recombination in Whole Bacterial Genomes

Introduction

In this tutorial we learn how to install clonalframeml on Debian 10.

What is `clonalframeml`

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

There are three methods to install clonalframeml on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install clonalframeml Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install clonalframeml using apt-get by running the following command:

sudo apt-get -y install clonalframeml

Install clonalframeml Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install clonalframeml using apt by running the following command:

sudo apt -y install clonalframeml

Install clonalframeml Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install clonalframeml using aptitude by running the following command:

sudo aptitude -y install clonalframeml

How To Uninstall clonalframeml on Debian 10

To uninstall only the clonalframeml package we can use the following command:

sudo apt-get remove clonalframeml

Uninstall clonalframeml And Its Dependencies

To uninstall clonalframeml and its dependencies that are no longer needed by Debian 10, we can use the command below:

sudo apt-get -y autoremove clonalframeml

Remove clonalframeml Configurations and Data

To remove clonalframeml configuration and data from Debian 10 we can use the following command:

sudo apt-get -y purge clonalframeml

Remove clonalframeml configuration, data, and all of its dependencies

We can use the following command to remove clonalframeml configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge clonalframeml

Dependencies

clonalframeml have the following dependencies:

References

Summary

In this tutorial we learn how to install clonalframeml package on Debian 10 using different package management tools: apt, apt-get and aptitude.