How To Install mptp on Ubuntu 22.04
Introduction
In this tutorial we learn how to install mptp on Ubuntu 22.04.
What is mptp
mptp is:
Implementation of a fast species delimitation method, based on PTP (Zhang et al. 2013) with a 64-bit multi-threaded design that handles very large datasets.
The tool mPTP can handle very large biodiversity datasets. It implements a fast method to compute the ML delimitation from an inferred phylogenetic tree of the samples. Using MCMC, it also computes the support values for each clade, which can be used to assess the confidence of the ML delimitation.
ML delimitation mPTP implements two flavours of the point-estimate solution. First, it implements the original method from (Zhang et al. 2013) where all within-species processes are modelled with a single exponential distribution. mPTP uses a dynamic programming implementation which estimates the ML delimitation faster and more accurately than the original PTP. The dynamic programming implementation has similar properties as (Gulek et al. 2010). See the wiki for more information. The second method assumes a distinct exponential distribution for the branching events of each of the delimited species allowing it to fit to a wider range of empirical datasets.
MCMC method mPTP generates support values for each clades. They represent the ratio of the number of samples for which a particular node was in the between-species process, to the total number of samples.
There are three methods to install mptp on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install mptp Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install mptp using apt-get by running the following command:
sudo apt-get -y install mptp
Install mptp Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install mptp using apt by running the following command:
sudo apt -y install mptp
Install mptp 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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install mptp using aptitude by running the following command:
sudo aptitude -y install mptp
How To Uninstall mptp on Ubuntu 22.04
To uninstall only the mptp package we can use the following command:
sudo apt-get remove mptp
Uninstall mptp And Its Dependencies
To uninstall mptp and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove mptp
Remove mptp Configurations and Data
To remove mptp configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge mptp
Remove mptp configuration, data, and all of its dependencies
We can use the following command to remove mptp configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge mptp
References
Summary
In this tutorial we learn how to install mptp package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
