How To Install dotter on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 550 words

Introduction

In this tutorial we learn how to install dotter on Ubuntu.

What is `dotter`

dotter is:

Dotter is a graphical dot-matrix program for detailed comparison of two sequences.

Every residue in one sequence is compared to every residue in the other, and a matrix of scores is calculated.
One sequence is plotted on the x-axis and the other on the y-axis.
Noise is filtered out so that alignments appear as diagonal lines.
Pairwise scores are averaged over a sliding window to make the score matrix more intelligible.
The averaged score matrix forms a three-dimensional landscape, with the two sequences in two dimensions and the height of the peaks in the third. This landscape is projected onto two dimensions using a grey-scale image - the darker grey of a peak, the higher the score is.
The contrast and threshold of the grey-scale image can be adjusted interactively, without having to recalculate the score matrix.
An Alignment Tool is provided to examine the sequence alignment that the grey-scale image represents.
Known high-scoring pairs can be loaded from a GFF file and overlaid onto the plot.
Gene models can be loaded from GFF and displayed alongside the relevant axis.
Compare a sequence against itself to find internal repeats.
Find overlaps between multiple sequences by making a dot-plot of all sequences versus themselves.
Run Dotter in batch mode to create large, time-consuming dot-plots as a background process.

There are three methods to install dotter 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 dotter Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install dotter using apt-get by running the following command:

sudo apt-get -y install dotter

Install dotter Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install dotter using apt by running the following command:

sudo apt -y install dotter

Install dotter 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 dotter using aptitude by running the following command:

sudo aptitude -y install dotter

How To Uninstall dotter on Ubuntu

To uninstall only the dotter package we can use the following command:

sudo apt-get remove dotter

Uninstall dotter And Its Dependencies

To uninstall dotter and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove dotter

Remove dotter Configurations and Data

To remove dotter configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge dotter

Remove dotter configuration, data, and all of its dependencies

We can use the following command to remove dotter configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge dotter

Dependencies

dotter have the following dependencies:

References

dotter website

Summary

In this tutorial we learn how to install dotter package on Ubuntu using different package management tools: apt, apt-get and aptitude.