How To Install gff2aplot on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
4 minutes • 661 words
Introduction
In this tutorial we learn how to install gff2aplot on Ubuntu.
What is gff2aplot
gff2aplot is:
A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot:
- Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets.
- All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file.
- Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement.
- All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients.
- Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes.
- The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error.
- gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape.
- You can draw different alignments on same alignment plot and distinguish them by using different colors for each.
- Shape dictionary has been expanded, so that further feature shapes are now available (see manual).
- Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows one to show color pseudo-blending when horizontal and vertical ribbons overlap.
There are three methods to install gff2aplot on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install gff2aplot Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install gff2aplot using apt-get by running the following command:
sudo apt-get -y install gff2aplot
Install gff2aplot Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install gff2aplot using apt by running the following command:
sudo apt -y install gff2aplot
Install gff2aplot 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 gff2aplot using aptitude by running the following command:
sudo aptitude -y install gff2aplot
How To Uninstall gff2aplot on Ubuntu
To uninstall only the gff2aplot package we can use the following command:
sudo apt-get remove gff2aplot
Uninstall gff2aplot And Its Dependencies
To uninstall gff2aplot and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove gff2aplot
Remove gff2aplot Configurations and Data
To remove gff2aplot configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge gff2aplot
Remove gff2aplot configuration, data, and all of its dependencies
We can use the following command to remove gff2aplot configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge gff2aplot
Dependencies
gff2aplot have the following dependencies:
References
Summary
In this tutorial we learn how to install gff2aplot package on Ubuntu using different package management tools: apt, apt-get and aptitude.