treetime | Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction | Machine Learning library

by neherlab Jupyter Notebook Version: v0.9.6 License: MIT

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | treetime Summary

treetime is a Jupyter Notebook library typically used in Artificial Intelligence, Machine Learning, Deep Learning applications. treetime has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence. 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 unconstrained 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 on the command-line or as a library used in larger phylogenetic analysis work-flows. The documentation of TreeTime is hosted on readthedocs.org. In addition to scripting TreeTime or using it via the command-line, there is also a small web server at treetime.ch. Have a look at our repository with example data and the tutorials.

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Quality

Security

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Support

treetime has a low active ecosystem.

It has 173 star(s) with 52 fork(s). There are 14 watchers for this library.

It had no major release in the last 12 months.

There are 20 open issues and 94 have been closed. On average issues are closed in 108 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of treetime is v0.9.6

Quality

treetime has 0 bugs and 0 code smells.

Security

treetime has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

treetime code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

treetime is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

treetime releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

treetime saves you 2728 person hours of effort in developing the same functionality from scratch.

It has 5902 lines of code, 313 functions and 27 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed treetime and discovered the below as its top functions. This is intended to give you an instant insight into treetime implemented functionality, and help decide if they suit your requirements.

Performs marginal reconstruction on the clock tree
Calculate peak value
Adjusts the grid according to the interpolation
Divide two values
Scan for homoplasylasies
Infer ancestral sequences
Infer GTR
Infer the state of the transition matrix
Create argument parser
Parse a datetime dat file
Performs the marginal reconstruction of the clock tree
Calculate the clock filter
Performs ancestral reconstruction
Assign date constraints to each node
Compute probabilistic probability for a sequence t
Set the tree
Compute probability at t
Infer root gtr
Set the precision
Generate the skyline of the trees
Calculates effective support for the peak
Propagate a profile onto a profile
Set the alignment
Assign rates to the site
Perform joint reconstruction of joint reconstruction
Extract a dictionary of strain dates
Manage mugration
Compute the clock filter
Create Fitch profiles

Get all kandi verified functions for this library.

treetime Key Features

No Key Features are available at this moment for treetime.

treetime Examples and Code Snippets

No Code Snippets are available at this moment for treetime.

Community Discussions

Trending Discussions on treetime

TypeError: list indices must be integers or slices not str

Apply drop down selection to tree view row

What is wrong with my insert BST implementation in Python?

QUESTION

TypeError: list indices must be integers or slices not str

Asked 2020-Aug-12 at 02:50

I cant get this to work, I have read other SO qs regarding this issue but I cant seem to find the info to suit my application. Im getting TypeError: list indices must be integers or slices not str Im holding my with open in a function as I only want to call it when a button is pressed. Im sure it has to do with for row in csv_file: do I need a for line in csv_file: then for row? Im stuck

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ANSWER

Answered 2020-Aug-12 at 02:50

You're accessing the row columns by field name, not index. To use field names, try the DictReader function.

Source https://stackoverflow.com/questions/63368395

QUESTION

Apply drop down selection to tree view row

Asked 2020-Aug-10 at 09:52

I want to create a function that will apply a drop-down box selection to a treeview row. Ideally by clicking on the desired row in the GUI, then selecting a value from the drop down selection StatusList. Then I would like to input the chosen drop down selection into the row that was clicked. The column to enter the drop-down selection in would be Current Status

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ANSWER

Answered 2020-Aug-10 at 09:52

You can use the command option of the OptionMenu to insert the chosen value in the treeview. It takes a function with one argument, which is the selected value, and this function is triggered each time the user selects a value in the OptionMenu. In this function, you need to get the currently selected row, which can be done with treetime.focus(), then change the value in the 'CurrentStatus' column, with treetime.set(, 'CurrentStatus', ):

Source https://stackoverflow.com/questions/63333819

QUESTION

What is wrong with my insert BST implementation in Python?

Asked 2020-Jun-10 at 13:08

I'm trying to implement BST, but the head value of my tree returns None every time. I've tried to look up other implementations in Python but they usually just declare a root and pass it in outside of the class itself instead of having the head self contained in the class.

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ANSWER

Answered 2020-Jun-10 at 13:08

As @MarkMeyer pointed out, currentNode = Node(data) only creates a local variable. Therefore you need to return curretNode variable to the caller and update the node by returned variable.

When you fix four lines (#1 to #4), you will get the desired result.

Source https://stackoverflow.com/questions/62250626

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install treetime

TreeTime is compatible with Python 3.6 upwards and is tested on 3.6, 3.7, and 3.8. It depends on several Python libraries:. You may install TreeTime and its dependencies by running. within this repository. You can also install TreeTime from PyPi via. You might need root privileges for system wide installation. Alternatively, you can simply use it TreeTime locally without installation. In this case, just download and unpack it, and then add the TreeTime folder to your $PYTHONPATH.
numpy, scipy, pandas: for all kind of mathematical operations as matrix operations, numerical integration, interpolation, minimization, etc.
BioPython: for parsing multiple sequence alignments and all phylogenetic functionality
matplotlib: optional dependency for plotting