A tool to find nonmonophyly in a phylogenetic tree.

• install docker: docker.com or brew install docker-ce (with https://brew.sh installed)

Two steps:

1. Either double-click the "hybsearch" file in the folder, or, with a terminal, cd into the hybsearch folder and run ./hybsearch.
2. Run docker run -p 8080:8080 -it hybsearch/hybsearch

If you don't have docker, TODO.

If you're on Windows, TODO.

You'll need Docker, still.

Any changes you make to the JS can be run by simply pressing ⌘R. There is no build process.

Whenever you change the data pipeline, you will need to rebuild the Docker image.

We recommend using a local Docker tag to test with; anywhere you would write hybsearch/hybsearch, you should just write hybsearch instead.

To rebuild the container:

docker build -t hybsearch .

To run your rebuilt container:

docker run -p 8080:8080 -it hybsearch

Our current versions of our dependencies:

• Docker: 17.20.x

Or

• Node: 8.x
• Beagle: 2.1.2
• OpenMPI: 2.1.1
• Clustal-Omega: 1.2.0
• MrBayes: 3.2.6
• Electron: 1.6.10
• seq-gen: 1.3.3
• seqmagick: 0.6.1

If you have Docker installed, all you need to do is (in the project root)

$ docker run --port 8080:8080 -it hybsearch/hybsearch
$ ./hybsearch

which will start the server that the electron app uses.

./vendor/seqmagick/cli.py convert --input-format fasta --output-format nexus --alphabet dna <input> <output>

• npm install -g electron-download
• electron-download --version=<version>
• Copy the zip from ~/.electron and extract it into hybsearch/vendor
• Edit the hybsearch file to point to the new path
• Remove the old folder

>>> hamming-distance speciesA speciesB
$minimumDistance
>>> estimate-generations $minimumDistance
{divergenceTime, generationCount}
>>> seq-gen $file --generations $generationCount
$sequences > sequences.fasta
>>> hamdis sequences.fasta
???