How to Install and Uninstall paleomix Package on Ubuntu 21.10 (Impish Indri)

Last updated: December 29,2024

1. Install "paleomix" package

Please follow the steps below to install paleomix on Ubuntu 21.10 (Impish Indri)


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

This tutorial shows how to uninstall paleomix on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                paleomix
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the paleomix package on Ubuntu 21.10 (Impish Indri)

Package: paleomix
Architecture: amd64
Version: 1.3.2-1
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: 1990
Depends: python3-coloredlogs, python3-configargparse, python3-pysam, python3-ruamel.yaml, python3-setproctitle, python3:any, adapterremoval, bedtools, bowtie2, bwa, bcftools, examl, mafft, mapdamage, phylip, picard-tools, r-base-core, radiant, raxml, samtools
Filename: pool/universe/p/paleomix/paleomix_1.3.2-1_amd64.deb
Size: 969248
MD5sum: e5813176697fde0bd3ee7731b8af5a47
SHA1: e2ebc129a1461fe49c61a5e2d964e24b1098370b
SHA256: 4aab5c704d93f3dff1dfe73f7276c96f41c86b8ef1fc62c36b421e3ba93c01e9
SHA512: 39afc3970792a097b58f7a353c8bb3db93ebe45ee83ba81892a37ac05382fb01d397b6202d9692fa70e223cc88b296881a4b3ef9f8df449e002720b7cf7794fb
Homepage: https://geogenetics.ku.dk/publications/paleomix
Description-en: pipelines and tools for the processing of ancient and modern HTS data
The PALEOMIX pipelines are a set of pipelines and tools designed to aid
the rapid processing of High-Throughput Sequencing (HTS) data: The BAM
pipeline processes de-multiplexed reads from one or more samples,
through sequence processing and alignment, to generate BAM alignment
files useful in downstream analyses; the Phylogenetic pipeline carries
out genotyping and phylogenetic inference on BAM alignment files, either
produced using the BAM pipeline or generated elsewhere; and the Zonkey
pipeline carries out a suite of analyses on low coverage equine
alignments, in order to detect the presence of F1-hybrids in
archaeological assemblages. In addition, PALEOMIX aids in metagenomic
analysis of the extracts.
.
The pipelines have been designed with ancient DNA (aDNA) in mind, and
includes several features especially useful for the analyses of ancient
samples, but can all be for the processing of modern samples, in order
to ensure consistent data processing.
Description-md5: 7cb3c4aa709e51b480a41a73961d7253