DendroPy | A Python library for phylogenetic scripting, simulation, data processing and manipulation

by jeetsukumaran Python Version: 5.0.1 License: Non-SPDX

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

kandi X-RAY | DendroPy Summary

DendroPy is a Python library. DendroPy has no bugs, it has no vulnerabilities, it has build file available and it has low support. However DendroPy has a Non-SPDX License. You can install using 'pip install DendroPy' or download it from GitHub, PyPI.

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

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Quality

Security

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Support

DendroPy has a low active ecosystem.

It has 185 star(s) with 59 fork(s). There are 13 watchers for this library.

It had no major release in the last 12 months.

There are 45 open issues and 78 have been closed. On average issues are closed in 98 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of DendroPy is 5.0.1

Quality

DendroPy has 0 bugs and 0 code smells.

Security

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

DendroPy code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

DendroPy has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

DendroPy releases are not available. You will need to build from source code and install.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Top functions reviewed by kandi - BETA

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

Fast birth and death trees
Creates a new child node
Clears all child nodes
List of child nodes
Compute the birth and death likelihood
Return a list of all internal nodes
Compute the survival probability of a constant
Calculates the age of each node
Generate a MRCA node
Encodes the bipartitions
Compute parsimony score
Create a new child node
Evolve a continuous character
Generate an upgma tree
Generate a phylogenetic tree for a given tree
Read pre - trained trees from target trees
Reroot the tree rooted at the root node
Parse the contents of the tree from a stream
Generate a random population tree
Creates a Kingman tree
Generate a discrete birth and death tree
Calculate the age of the node
Generate a phylogenetic tree
Read taxon data from csv file
Summarize splits on a tree
Extract a tree
Encode the bipartitions
Create a TreeCollection from a stream

Get all kandi verified functions for this library.

DendroPy Key Features

No Key Features are available at this moment for DendroPy.

DendroPy Examples and Code Snippets

No Code Snippets are available at this moment for DendroPy.

Community Discussions

Trending Discussions on DendroPy

Printing tip labels when using the python module dendropy to calculate pairwise distances between nodes on a phylogenetic tree?

How to extract patristic distances from dendropy phylogenetic_distance_matrix

Specify Python 2.7+ and Python 3.xx (any) in ``setup.py''

QUESTION

Printing tip labels when using the python module dendropy to calculate pairwise distances between nodes on a phylogenetic tree?

Asked 2019-Jun-20 at 08:16

I'm trying to create an array in python that will contain all the pairwise distances between every pair of nodes on a phylogenetic tree. I'm currently using dendropy to do this. (I initially looked at biopython but couldn't find an option to do this). The code I have so far looks like this:

...

ANSWER

Answered 2017-Apr-04 at 14:46

Converting the tip labels to a string converted them to the name surrounded by speech marks, e.g.:

Source https://stackoverflow.com/questions/43065864

QUESTION

How to extract patristic distances from dendropy phylogenetic_distance_matrix

Asked 2018-Nov-28 at 15:42

I have created a cophenetic distance matrix in dendropy using:

...

ANSWER

Answered 2018-Nov-28 at 15:42

as_data_table() returns an object of type dendropy.utility.container.DataTable. This DataTable is a custom container class, which implements lots of useful methods you can use to get at your data. You can read the source here to understand it:

https://dendropy.org/_modules/dendropy/utility/container.html

You can very quickly see the data in a format you can understand by looking at its _data variable:

Source https://stackoverflow.com/questions/53522836

QUESTION

Specify Python 2.7+ and Python 3.xx (any) in ``setup.py''

Asked 2017-Jan-14 at 17:58

My "setup.py" currently includes the following statement:

...

ANSWER

Answered 2017-Jan-14 at 17:58

The classifiers are just hints, neither conda install or pip install actually looks at them when you install a package. These hints are for the people searching for a package or looking at a package. If a package supports all python 3 versions it doesn't matter if you list them explicitly or just as "Programming Language :: Python :: 3" I guess most visitors will know what's meant - it's more a matter of personal preference of the author (and the number of already chosen classifiers).

However when you install the package with conda (even if it's pure python) it has to built against the python and OS version you're using. In your case you try to install from the ericmjl conda channel. This channel contains the python 3.5 version but only for OSX, the binaries for linux are python 3.4 only.

You could install it from PyPI into your conda environment by using pip: pip install dendropy (make sure you use the pip that's installed in your conda environment).

Source https://stackoverflow.com/questions/41642066

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

Vulnerabilities

No vulnerabilities reported

Install DendroPy

You can install using 'pip install DendroPy' or download it from GitHub, PyPI.
You can use DendroPy like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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