bacter | Bacterial phylogenetics in BEAST

by tgvaughan Java Version: v2.2.3 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | bacter Summary

bacter is a Java library. bacter has a Strong Copyleft License and it has low support. However bacter has 5 bugs, it has 2 vulnerabilities and it build file is not available. You can download it from GitHub.

Bacter is a [BEAST 2] package which facilitates inference of a (restricted kind of) ancestral recombination graph (ARG) and related parameters from a sequence alignment. It is based on the model described in [Didelot et al.'s 2010 Genetics paper][1]. This archive contains the source code of the package and is therefore of primary interest to programmers. For installation and usage instructions, as well as links to tutorials and other documentation, please visit the project home page hosted at

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Quality

Security

License

Reuse

Support

bacter has a low active ecosystem.

It has 14 star(s) with 6 fork(s). There are 13 watchers for this library.

It had no major release in the last 12 months.

There are 1 open issues and 24 have been closed. On average issues are closed in 77 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of bacter is v2.2.3

Quality

bacter has 5 bugs (1 blocker, 1 critical, 1 major, 2 minor) and 593 code smells.

Security

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

bacter code analysis shows 2 unresolved vulnerabilities (2 blocker, 0 critical, 0 major, 0 minor).

There are 12 security hotspots that need review.

License

bacter is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

bacter releases are available to install and integrate.

bacter has no build file. You will be need to create the build yourself to build the component from source.

bacter saves you 7072 person hours of effort in developing the same functionality from scratch.

It has 14641 lines of code, 584 functions and 127 files.

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

Top functions reviewed by kandi - BETA

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

Calculate a Conversion
Draw the affected region
Calculates the probability of an affected region
Obtain redundant conversions
Summarize all conversions of a given ACG
Returns a list of contiguous regions that have been covered by the specified locus
Applies the proposal to this operator
Returns true if the source node is invalid
Main method for testing
Disconnect an edge from the given node
Print this node
This method initializes the internal structures
Run the loop
Selects a new conversion
Initialize the acgistic variables
Calculates the logp value
Calculates the proposal
Returns an iterator over the conversion graph
Returns a copy of this ConversionGraph object
Apply a swap to the swap
Write the gene flow statistics to a file
Returns an iterator that iterates all the ACGs in the log file
Demonstrates how to read the true ARG file
Returns the proposal
Entry point for debugging
Computes the proposed height for a new node

Get all kandi verified functions for this library.

bacter Key Features

No Key Features are available at this moment for bacter.

bacter Examples and Code Snippets

No Code Snippets are available at this moment for bacter.

Community Discussions

Trending Discussions on bacter

How to gsub string with any partially matched string

QUESTION

How to gsub string with any partially matched string

Asked 2019-Sep-22 at 15:24

I have my string as:

...

ANSWER

Answered 2019-Sep-22 at 03:58

We can use sub and replace from "Bact" till the first semi-colon with "Bctr";

Source https://stackoverflow.com/questions/58045870

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

Vulnerabilities

No vulnerabilities reported

Install bacter

You can download it from GitHub.
You can use bacter like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the bacter component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

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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