Releases: bioDS/beast-phylonco
Releases · bioDS/beast-phylonco
Phylonco v1.0.1
Requirements
- BEAST version 2.7.3 or greater
- BEASTLabs version 2.0.0 or greater
- lphybeast version 1.0.0 or greater
- lphybeast requires LPhy version 1.4.0
Release notes
- Update examples for BEAST v2.7
- Added Beauti templates for substitution models
GT16SubstitutionModel
,BinarySubstitutionModel
,MethylationHKY
- Added README instructions for Beauti
Setup instructions
BEAST2 with phylonco:
- See the user guide https://github.com/bioDS/beast-phylonco/blob/v1.0.1/README.md
LPhy and LPhyBeast:
- See LPhy and LPhyBEAST setup
- See Phylonco LPhy extension setup
- LPhy documentation phylonco-lphy/doc/index.md
- Examples see phylonco-lphy-examples.zip
Phylonco v1.0.0
Requirements
- BEAST version 2.7.3 or greater
- BEASTLabs version 2.0.0 or greater
- lphybeast version 1.0.0 or greater
Release notes
- Beagle support added in BeagleTreeLikelihoodWithError class
- To run Beagle with GPU use
./beast -beagle_GPU <beast xml>
This release is not compatible with BEAST v2.6
Setup instructions
BEAST2 with phylonco:
- See the user guide https://github.com/bioDS/beast-phylonco/blob/8cb0a404b9c5d8e76b65a6c30177d17395d52b3a/README.md
LPhy and LPhyBeast:
- See LPhy and LPhyBEAST setup
- See Phylonco LPhy extension setup
- LPhy documentation phylonco-lphy/doc/index.md
- Examples see phylonco-lphy-examples.zip
Phylonco v0.0.7
Requirements
- Beast2 version 2.6.7 or greater
- BEASTLabs version 1.9.7 or greater
- lphybeast version 0.4.1 or greater
Release notes
- Update compatibility to LPhy v1.3.1
- Fixed GT16ErrorModel annotations and citations
- Compatible with LPhy v1.3.1 and LPhyBeast v0.4.1
- For available LPhy functions see lphy/doc/index.md
Setup instructions
BEAST2 with phylonco:
- See the user guide https://github.com/bioDS/beast-phylonco/blob/v0.0.7-pre/README.md
LPhy and LPhyBeast:
- See requirements in https://github.com/LinguaPhylo/linguaPhylo/releases/tag/1.3.1
- Download and unzip the LPhy v1.3.1 release https://github.com/LinguaPhylo/linguaPhylo/releases/tag/1.3.1
- Download and move phylonco-lphy-0.0.*.jar to your LPhy install directory
lphystudio-1.3.1/lib
- For LPhyBeast setup see https://linguaphylo.github.io/setup/
- To launch LPhy, navigate to your
lphystudio-1.3.1
directory then run
java -p lib -m lphystudio
Phylonco v0.0.6
Requirements
- Beast2 version 2.6.6 or greater
- BEASTLabs version 1.9.7 or greater
- lphybeast version 0.3.0 or greater
Release notes
- Fix error message when running BEAST2 with Beagle installed
- Added BEAUti support for Binary substitution model
- Made examples more robust by adding parameter bounds
- Gradle builds now replace Ant builds
- Added compatibility with LPhy v1.2.0 and LPhyBeast v0.3.0
- For available LPhy functions see lphy/doc/index.md
Setup instructions
BEAST2 with phylonco:
- See the user guide https://github.com/bioDS/beast-phylonco/blob/v0.0.6/README.md
LPhy and LPhyBeast:
- See requirements in https://github.com/LinguaPhylo/linguaPhylo/releases/tag/1.2.0
- Download and unzip the LPhy v1.2.0 release https://github.com/LinguaPhylo/linguaPhylo/releases/tag/1.2.0
- Download and move phylonco-lphy-0.0.1.jar to your LPhy install directory
lphystudio-1.2.0/lib
- For LPhyBeast setup see https://linguaphylo.github.io/setup/
- To launch LPhy, navigate to your
lphystudio-1.2.0
directory then run
java -p lib -m lphystudio
Phylonco v0.0.5
Requirements
- Beast2 version 2.6.5 or greater
- BEASTLabs version 1.9.0 or greater
Release notes
- Faster tree likelihood calculation with error models
- Fixed ambiguity mappings in Binary and GT16 substitution models
- Added more unit tests for datatypes and error models
- Updated readme instructions
Phylonco v0.0.4
Requirements
- Beast2 version 2.6.5 or greater
- BEASTLabs version 1.9.0 or greater
Release notes
This Phylonco release includes the following features.
Error models:
- GT16 diploid nucleotide error model (16 states) with allelic dropout and sequencing/amplification errors
- Nucleotide error model (4 states - A, G, C, T) with a single error parameter epsilon and tips (1-e, e/3, e/3, e/3)
- General error model (n states) with a single error parameter epsilon; generalises the nucleotide error model to n states
- Binary error model of false positive and false negative errors
Substitution models:
- GT16 phased diploid nucleotide model (16 states)
- Binary substitution model
- SiFit substitution models (2 or 3 states)