How To Install phyml on Ubuntu 22.04
Introduction
In this tutorial we learn how to install phyml on Ubuntu 22.04.
What is phyml
phyml is:
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test).
PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long.
This package also includes PhyTime.
There are three methods to install phyml 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 phyml Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install phyml using apt-get by running the following command:
sudo apt-get -y install phyml
Install phyml Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install phyml using apt by running the following command:
sudo apt -y install phyml
Install phyml 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 phyml using aptitude by running the following command:
sudo aptitude -y install phyml
How To Uninstall phyml on Ubuntu 22.04
To uninstall only the phyml package we can use the following command:
sudo apt-get remove phyml
Uninstall phyml And Its Dependencies
To uninstall phyml and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove phyml
Remove phyml Configurations and Data
To remove phyml configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge phyml
Remove phyml configuration, data, and all of its dependencies
We can use the following command to remove phyml configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge phyml
References
Summary
In this tutorial we learn how to install phyml package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
