How to Install and Uninstall python3-treetime Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: May 22,2024

1. Install "python3-treetime" package

This guide covers the steps necessary to install python3-treetime on Ubuntu 20.10 (Groovy Gorilla)


    
        
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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 instructions below to uninstall python3-treetime on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                python3-treetime
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the python3-treetime package on Ubuntu 20.10 (Groovy Gorilla)

Package: python3-treetime
Architecture: all
Version: 0.7.5-1
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: 499
Depends: python3-biopython, python3-numpy, python3-pandas, python3-scipy, python3:any
Recommends: python3-matplotlib
Filename: pool/universe/p/python-treetime/python3-treetime_0.7.5-1_all.deb
Size: 106584
MD5sum: 39bc51647f8163bf1f765578611196a6
SHA1: 84b2a3b0bee9bbe288075cd37eaa3cddfe2c7601
SHA256: c5cc0df6688d6c504e2db2ddfeb82e9b2ee364f808d9ec273be4cbf8cc7f4462
SHA512: 5243f0bb8619f7acc4c0e6777710bff1d2d40bd0a7e338d32bc1826b3ee4822758bf84b38516d86894ad176daca05125afe1bcd4783b12e95d005ce0defbff46
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