How to Install and Uninstall staden Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: May 03,2024

1. Install "staden" package

Here is a brief guide to show you how to install staden on Ubuntu 20.10 (Groovy Gorilla)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                staden
            
                    
    
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2. Uninstall "staden" package

This tutorial shows how to uninstall staden on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                staden
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the staden package on Ubuntu 20.10 (Groovy Gorilla)

Package: staden
Architecture: amd64
Version: 2.0.0+b11-4build2
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 4423
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), liblzma5 (>= 5.1.1alpha+20120614), libpng16-16 (>= 1.6.2-1), libstaden-read14 (>= 1.14.12), libstdc++6 (>= 5), libtcl8.6 (>= 8.6.0), libtk8.6 (>= 8.6.0), libx11-6, zlib1g (>= 1:1.1.4), staden-common (= 2.0.0+b11-4build2), staden-io-lib-utils, tklib
Recommends: med-config (>= 2.1)
Filename: pool/universe/s/staden/staden_2.0.0+b11-4build2_amd64.deb
Size: 1412476
MD5sum: c4affb8a50dfad692ed742d51c4f632b
SHA1: c4844e0a841ccdf3786ddb29b04e6813063ad3dd
SHA256: 558a8e3e140cf1536b880883674738db004218732f91bb0a44118b57b63a7924
SHA512: 70252513aae18601b2aa6683976389196d77908c5b8a4f449dfec097c8542ecb49dd4a032c6ebfb6fb099066d702ce9070188fc1f1501474ed1ceb4f764d2e20
Homepage: https://sourceforge.net/projects/staden/
Description-en: DNA sequence assembly (Gap4/Gap5), editing and analysis tools
Staden is a fully developed set of DNA sequence assembly (Gap4 and
Gap5), editing and analysis tools (Spin).
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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.
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Pregap4 provides a graphical user interface to set up the processing
required to prepare trace data for assembly or analysis, and automates
these processes.
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Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
ZTR trace files.
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Prefinish analyses partially completed sequence assemblies and suggests
the most efficient set of experiments to help finish the project.
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Tracediff and hetscan automatically locate mutations by comparing trace
data against reference traces. They annotate the mutations found ready
for viewing in gap4.
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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.
Description-md5: ab389488bbaa41331fbf3a76064bea10