How To Install clonalframeml on Kali Linux
Introduction
In this tutorial we learn how to install clonalframeml on Kali Linux.
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 Kali Linux. 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 updateAfter updating apt database, We can install clonalframeml using apt-get by running the following command:
sudo apt-get -y install clonalframemlInstall clonalframeml Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install clonalframeml using apt by running the following command:
sudo apt -y install clonalframemlInstall clonalframeml Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install clonalframeml using aptitude by running the following command:
sudo aptitude -y install clonalframemlHow To Uninstall clonalframeml on Kali Linux
To uninstall only the clonalframeml package we can use the following command:
sudo apt-get remove clonalframemlUninstall clonalframeml And Its Dependencies
To uninstall clonalframeml and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove clonalframemlRemove clonalframeml Configurations and Data
To remove clonalframeml configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge clonalframemlRemove 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 clonalframemlDependencies
clonalframeml have the following dependencies:
References
Summary
In this tutorial we learn how to install clonalframeml package on Kali Linux using different package management tools: apt, apt-get and aptitude.