OrthoFinder | Phylogenetic orthology inference for comparative genomics | Genomics library

by davidemms Python Version: 2.5.5 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | OrthoFinder Summary

OrthoFinder is a Python library typically used in Artificial Intelligence, Genomics applications. OrthoFinder has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Downloading and running OrthoFinder. Running an example OrthoFinder analysis.

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Quality

Security

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Support

OrthoFinder has a low active ecosystem.

It has 549 star(s) with 178 fork(s). There are 25 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 203 open issues and 601 have been closed. On average issues are closed in 69 days. There are 10 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of OrthoFinder is 2.5.5

Quality

OrthoFinder has 0 bugs and 0 code smells.

Security

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

OrthoFinder code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

OrthoFinder 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

OrthoFinder releases are available to install and integrate.

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

Installation instructions, examples and code snippets are available.

It has 10235 lines of code, 691 functions and 34 files.

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

Top functions reviewed by kandi - BETA

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

Process command line arguments
Exit the task manager
Stops the worker process
Return the directory argument
Runs the tree
Retrieve the concatenated file concatenated sequenceAlignments
Retrieves the name of a species tree unrooted
Returns the root of the species tree
Runs the search command
Sort a CSV file
Read species information from seqsInfo file
Initialises a file handler
Checks options
Processes the log file
Processes a tree of trees
Run commands and move them
Compute the Robinson - Foulds between two trees
Calculate satifactory f
Main function
Retrieves the orthogonal results file
Create a primary transcript file
Process BLAST results
Creates a new node
Processes new FASTA files
Main function for the _orthologs method
Perform Orthogroups algorithm

Get all kandi verified functions for this library.

OrthoFinder Key Features

No Key Features are available at this moment for OrthoFinder.

OrthoFinder Examples and Code Snippets

No Code Snippets are available at this moment for OrthoFinder.

Community Discussions

Trending Discussions on OrthoFinder

Building queries with a cross database join using SQLalchemy ORM and SQLite

ggplot : several histogram as one

QUESTION

Building queries with a cross database join using SQLalchemy ORM and SQLite

Asked 2017-Nov-03 at 11:29

I have two SQLite databases containing tables I need to join using SQLalchemy. For reasons I can not combine all the tables into one SQLite database. I am using SQLalchemy ORM. I have not been able to find any solution online that meets my specific case.

My question is in principle the same as SQLAlchemy error query join across database, but the original poster's problem was solved using a different solution that does not match my use case.

My question to the wise people at Stackoverflow:

I want to emulate the following SQL query:

...

ANSWER

Answered 2017-Nov-03 at 11:29

Answer to my own question (thanks to Ilja for finding the solution):

I can define the engine like this:

Source https://stackoverflow.com/questions/47093551

QUESTION

ggplot : several histogram as one

Asked 2017-Jul-15 at 13:39

I want to plot the results of a benchmark of several bioinformatics tools, using ggplot. I would like t have all the bars on the same graph instead of having one graph for each tool. I already have an output with LibreOffice (see image below), but I want to re-do it with ggplot.

For now I have this kind of code for each tool (example with the first one) :

...

ANSWER

Answered 2017-Jul-15 at 13:39

Maybe this can help you in the right direction:

Source https://stackoverflow.com/questions/45118408

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

Vulnerabilities

No vulnerabilities reported

Install OrthoFinder

You can find a step-by-step tutorial here: Downloading and checking OrthoFinder including instructions for Mac, for which Bioconda is recommended and Windows, for which the Windows Subsystem for Linux is recommended. There are also tutorials on that site which guide you through running your first analysis and exploring the results files.

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 .

Find more information at: