Introduction
In this tutorial we learn how to install staden on Kali Linux.
What is staden
staden is:
Staden is a fully developed set of DNA sequence assembly (Gap4 and
Gap5), editing and analysis tools (Spin).
Gap4 performs sequence assembly, contig ordering based on read pair
data, contig joining based on sequence comparisons, assembly checking,
repeat searching, experiment suggestion, read pair analysis and contig
editing. It has graphical views of contigs, templates, readings and
traces which all scroll in register. Contig editor searches and
experiment suggestion routines use confidence values to calculate the
confidence of the consensus sequence and hence identify only places
requiring visual trace inspection or extra data. The result is
extremely rapid finishing and a consensus of known accuracy.
Pregap4 provides a graphical user interface to set up the processing
required to prepare trace data for assembly or analysis, and automates
these processes.
Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
ZTR trace files.
Prefinish analyses partially completed sequence assemblies and suggests
the most efficient set of experiments to help finish the project.
Tracediff and hetscan automatically locate mutations by comparing trace
data against reference traces. They annotate the mutations found ready
for viewing in gap4.
Spin analyses nucleotide sequences to find genes, restriction sites,
motifs, etc. It can perform translations, find open reading frames,
count codons, etc. Many results are presented graphically and a sliding
sequence window is linked to the graphics cursor. Spin also compares
pairs of sequences in many ways. It has very rapid dot matrix analysis,
global and local alignment algorithms, plus a sliding sequence window
linked to the graphical plots. It can compare nucleic acid against
nucleic acid, protein against protein, and protein against nucleic
acid.
There are three methods to install staden on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install staden Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install staden using apt-get by running the following command:
sudo apt-get -y install stadenInstall staden Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install staden using apt by running the following command:
sudo apt -y install stadenInstall staden Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install staden using aptitude by running the following command:
sudo aptitude -y install staden
How To Uninstall staden on Kali Linux
To uninstall only the staden package we can use the following command:
sudo apt-get remove staden
Uninstall staden And Its Dependencies
To uninstall staden and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove staden
Remove staden Configurations and Data
To remove staden configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge staden
Remove staden configuration, data, and all of its dependencies
We can use the following command to remove staden configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge staden
Dependencies
staden have the following dependencies:
References
Summary
In this tutorial we learn how to install staden package on Kali Linux using different package management tools: apt, apt-get and aptitude.
