OrthoFinder | Phylogenetic orthology inference for comparative genomics | Genomics library

 by   davidemms Python Version: 2.5.5 License: GPL-3.0

kandi X-RAY | OrthoFinder Summary

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.

            kandi-support 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

            kandi-Quality Quality

              OrthoFinder has 0 bugs and 0 code smells.

            kandi-Security 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.

            kandi-License 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.

            kandi-Reuse 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


            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:



            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


            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) :



            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


            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.


            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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