tdg09 | data used in Tamuri AU
kandi X-RAY | tdg09 Summary
kandi X-RAY | tdg09 Summary
tdg09 is a Java library. tdg09 has no bugs, it has no vulnerabilities and it has low support. However tdg09 build file is not available. You can download it from GitHub.
This program is an implementation of the model described in:. Tamuri AU, dos Reis M, Hay AJ, Goldstein RA (2009) Identifying Changes in Selective Constraints: Host Shifts in Influenza. PLoS Comput Biol 5(11): e1000564. doi:10.1371/journal.pcbi.1000564. This phylogenetic model uses site-specific amino acid frequencies to distinguish patterns of substitution between two (or more) lineages or groups of taxa. We first estimate the site-specific amino acid frequencies at a given location in a protein alignment assuming that the pattern of substitution is homogeneous across all branches. We then estimate multiple sets of site-specific frequencies, allowing them to differ among different branches, producing a non-homogeneous model of evolutionary change. Using statistical tests, we then see whether the non-homogeneous model provides a significantly better fit to the data than the homogenous model.
This program is an implementation of the model described in:. Tamuri AU, dos Reis M, Hay AJ, Goldstein RA (2009) Identifying Changes in Selective Constraints: Host Shifts in Influenza. PLoS Comput Biol 5(11): e1000564. doi:10.1371/journal.pcbi.1000564. This phylogenetic model uses site-specific amino acid frequencies to distinguish patterns of substitution between two (or more) lineages or groups of taxa. We first estimate the site-specific amino acid frequencies at a given location in a protein alignment assuming that the pattern of substitution is homogeneous across all branches. We then estimate multiple sets of site-specific frequencies, allowing them to differ among different branches, producing a non-homogeneous model of evolutionary change. Using statistical tests, we then see whether the non-homogeneous model provides a significantly better fit to the data than the homogenous model.
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tdg09 has a low active ecosystem.
It has 2 star(s) with 2 fork(s). There are no watchers for this library.
It had no major release in the last 12 months.
There are 1 open issues and 0 have been closed. There are 1 open pull requests and 0 closed requests.
It has a neutral sentiment in the developer community.
The latest version of tdg09 is v1.1.2
Quality
tdg09 has 0 bugs and 0 code smells.
Security
tdg09 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
tdg09 code analysis shows 0 unresolved vulnerabilities.
There are 0 security hotspots that need review.
License
tdg09 does not have a standard license declared.
Check the repository for any license declaration and review the terms closely.
Without a license, all rights are reserved, and you cannot use the library in your applications.
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tdg09 releases are available to install and integrate.
tdg09 has no build file. You will be need to create the build yourself to build the component from source.
Installation instructions are not available. Examples and code snippets are available.
Top functions reviewed by kandi - BETA
kandi has reviewed tdg09 and discovered the below as its top functions. This is intended to give you an instant insight into tdg09 implemented functionality, and help decide if they suit your requirements.
- Main method for testing
- Run the WAG algorithm on the phylo alignment
- Gets the parameters for minimisation
- Returns an array of equilibrium frequencies
- Print the parameters
- Convert amino acids to parameters
- Reads the tree from the given file path
- Read the alignment
- Performs the algorithm and returns the result
- Converts a list of parameters into a model
- Adds all the constraints to the given min and upper bounds
- Runs the minimisation
- Loads the sequence at the specified site and stores it in the sequence
- Converts a tree node node to a file
Get all kandi verified functions for this library.
tdg09 Key Features
No Key Features are available at this moment for tdg09.
tdg09 Examples and Code Snippets
No Code Snippets are available at this moment for tdg09.
Community Discussions
No Community Discussions are available at this moment for tdg09.Refer to stack overflow page for discussions.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install tdg09
You can download it from GitHub.
You can use tdg09 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 tdg09 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 .
You can use tdg09 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 tdg09 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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