gophy

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View the Project on GitHub FePhyFoFum/gophy

gophy is not finished and may never be. It serves as a phylogenetic development toolkit from which to make tests and tools for a variety of purposes.

installation

Installation of gophy is much like most other github developed go based packages. If you have not setup or installed go before, I recommend you check installation instructions out here. Once you have setup your environment, then you can obtain gophy like any other go package: go get github.com/FePhyFoFum/gophy. This will get all of the dependencies with it. To update it if you already have it installed, you can type go get -u github.com/FePhyFoFum/gophy or you can update all of your go packages (this might be good at least for gonum that will come with gophy) you can type go get -u all.

some useful packages

While gophy is not finished, there are several tools that you may use. Here is a description of how to compile and use those packages.

bp

bp is a bipartition analyzer. It does a lot of things and pretty quickly. First, to build it, you run go build github.com/FePhyFoFum/gophy/bp/bp.go. That will make an executable called bp. You can move that to your PATH or just type the full path to use it. Some features include

Here are some examples of some runs that you can do with bp.

Pairwise comparisons: You can compare all the trees in a file to each other bp -t t -pc or to a pool of biparts made from the trees in the file bp -t t -pca.

Map concordance and conflict: bp can take a list of trees, say in a file t and map whether bipartitions are concordant, conflicting, or uninformative (based on support or branch length) to another file with a single tree, say in a file t1. You run this with bp -t t -c t1. This will give a list of the biparts from t1 and for each that have conflict list the conflicting ones from t with the number that conflict (the number in parentheses is just an id for the bipart). If you want to spit out a set of trees with the internal nodes representing conflict, concordance, and uninformative, do bp -t t -c t1 -tv. You will get the same output and then a line that says “TREES WITH CONFLICT (FIRST), CONCORDANCE (SECOND), UNSUPPORTED (THIRD), PROPS AFTER” and 6 trees. The first is the number of conflicting trees, concordant trees, and unsupported trees (because of support or branch length cutoffs). The next three are the same order but instead of number, they are proportions. If you have a big file you can do bp -t t -c t1 -w 100 -tv to create a bunch of workers and use multicore. The number of workers is not the number of cores. I generally do ~100.

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