How to Install and Uninstall python3-treetime Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 18,2024

1. Install "python3-treetime" package

Please follow the guidelines below to install python3-treetime on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                python3-treetime
            
                    
    
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2. Uninstall "python3-treetime" package

Please follow the guidance below to uninstall python3-treetime on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                python3-treetime
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the python3-treetime package on Ubuntu 21.10 (Impish Indri)

Package: python3-treetime
Architecture: all
Version: 0.8.1-1
Priority: optional
Section: universe/python
Source: python-treetime
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 487
Depends: python3-biopython, python3-numpy, python3-pandas, python3-scipy, python3:any
Recommends: python3-matplotlib
Filename: pool/universe/p/python-treetime/python3-treetime_0.8.1-1_all.deb
Size: 102844
MD5sum: 3eb7e605db10fe53b44bb4cc7343aa24
SHA1: 134eb60ad8359f7e569e2d9f929b088e413b0a58
SHA256: 0414c21b238153f9c88db4b527fc4b2a116a45e6ae118d193eac192357c9b847
SHA512: e345d240f2fc4688576f68875717564580438c64134a0b8a0a32f0d427f83f37a0f2921a11249561476a63455cd94866792371bea632fe5093fd9fe6cbd4db7b
Homepage: https://github.com/neherlab/treetime
Description-en: inference of time stamped phylogenies and ancestral reconstruction (Python 3)
TreeTime provides routines for ancestral sequence reconstruction and the
maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
where all branches are scaled such that the locations of terminal nodes
correspond to their sampling times and internal nodes are placed at the
most likely time of divergence.
.
TreeTime aims at striking a compromise between sophisticated
probabilistic models of evolution and fast heuristics. It implements GTR
models of ancestral inference and branch length optimization, but takes
the tree topology as given. To optimize the likelihood of time-scaled
phylogenies, treetime uses an iterative approach that first infers
ancestral sequences given the branch length of the tree, then optimizes
the positions of unconstraine d nodes on the time axis, and then repeats
this cycle. The only topology optimization are (optional) resolution of
polytomies in a way that is most (approximately) consistent with the
sampling time constraints on the tree. The package is designed to be
used as a stand-alone tool or as a library used in larger phylogenetic
analysis workflows.
.
Features
* ancestral sequence reconstruction (marginal and joint maximum
likelihood)
* molecular clock tree inference (marginal and joint maximum
likelihood)
* inference of GTR models
* rerooting to obtain best root-to-tip regression
* auto-correlated relaxed molecular clock (with normal prior)
.
This package provides the Python 3 module.
Description-md5: 08684c07bc46e3c9a45e193598335689