Phylonco v1.2.1

In this release phylonco-beast and phylonco-lphy-studio are the same as the previous release (v1.2.0).

Requirements

BEAST

• phylonco (beast package) requires BEAST version 2.7.6 or greater
• phylonco (beast package) requires BEASTLabs version 2.0.2 or greater

LPhy and LPhyBeast

• phylonco-lphy requires LPhy version 1.6.1 or greater
• phylonco.lphybeast (beast package) requires LPhyBeast version 1.2.1 or greater

LPhy examples: phylonco-lphy-1.2.0-examples.zip

LPhy documentation: phylonco-lphy doc

Release notes

LPhy and LPhyBeast

• File naming changes

Setup instructions

The phylonco and phylonco.lphybeast packages can be installed using Beauti package manager.

For LPhy installation, the two jars phylonco-lphy-1.2.1.jar and phylonco-lphy-studio-1.2.0.jar need to be copied to the lib subdirectory of your LPhy installation. See setup instructions and the extension installation guide.

Phylonco v1.2.0

Requirements

BEAST

• BEAST version 2.7.6 or greater
• BEASTLabs version 2.0.2 or greater

LPhy and LPhyBeast

• LPhy version 1.6.0 or greater
• LPhyBeast version 1.2.0 or greater

LPhy examples: phylonco-lphy-1.2.0-examples.zip

LPhy documentation: phylonco-lphy doc

Release notes

BEAST

• Coalescent model with Gompertz population growth (f0 and t50 parameterizations)
• Coalescent model with logistic population growth
• Coalescent model with model averaging by stochastic variable selection (constant, exponential, logistic, Gompertz)
• Phylonco is now split into separate releases for beast, lphy and lphybeast
• Fix version compatibility issue with LPhy and LPhyBeast
• Build now uses Maven instead of Gradle
• Gompertz example manually patched

LPhy and LPhyBeast

• haploid function for converting genotypes to haploid alleles
• LPhyBeast to XML converters for coalescent population function models and model averaging
• Some LPhy examples manually patched

Setup instructions

The phylonco (beast) and phylonco.lphybeast (lphybeast) packages can be installed using Beauti package manager.

For LPhy installation, the two jars phylonco-lphy-1.2.0.jar and phylonco-lphy-studio-1.2.0.jar need to be copied to the lib subdirectory of your LPhy installation. See setup instructions and the extension installation guide.

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)