How To Install pftools on Ubuntu 22.04
Introduction
In this tutorial we learn how to install pftools on Ubuntu 22.04.
What is pftools
pftools is:
The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases.
File formats used by the pftools
- Generalized profiles format and syntax.
- The multiple sequence alignment format (PSA).
- The extended header multiple sequence alignment format (XPSA).
Programs to build generalized profiles pfmake Build a profile from a multiple sequence alignment. pfscale Fit parameters of an extreme-value distribution to a profile score list. pfw Weight sequences of a multiple sequence alignment to correct for sampling bias.
Programs to search with generalized profiles pfsearch / pfsearchV3 Search a protein or DNA sequence library for sequence segments matching a profile (V3 is the new version of this tool). pfscan Scan a protein or DNA sequence with a profile library
Conversion programs psa2msa Reformat PSA file to Pearson/Fasta multiple sequence alignment file. ptof Convert a protein profile into a frame-search profile to search DNA sequences. To be used with 2ft. 2ft Converts both strands of DNA into so-called interleaved frame-translated DNA sequences to search with protein profiles. To be used with ptof. 6ft Translates all six reading frames of a double-stranded DNA sequence into individual protein sequences. pfgtop Convert a profile in GCG format into PROSITE format. pfhtop Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile. ptoh Converts a generalized profile into an approximately equivalent HMM profile in HMMER1 format (can be read by the hmmconvert program from the HMMER2 package).
There are three methods to install pftools 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 pftools Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pftools using apt-get by running the following command:
sudo apt-get -y install pftools
Install pftools Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pftools using apt by running the following command:
sudo apt -y install pftools
Install pftools 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 pftools using aptitude by running the following command:
sudo aptitude -y install pftools
How To Uninstall pftools on Ubuntu 22.04
To uninstall only the pftools package we can use the following command:
sudo apt-get remove pftools
Uninstall pftools And Its Dependencies
To uninstall pftools and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove pftools
Remove pftools Configurations and Data
To remove pftools configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge pftools
Remove pftools configuration, data, and all of its dependencies
We can use the following command to remove pftools configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pftools
References
Summary
In this tutorial we learn how to install pftools package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.