gotree

GoTree

GoTree is a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language.

The goal is to handle phylogenetic trees in Newick format, through several basic commands. Each command may print result (a tree for example) in the standard output, and thus can piped to the standard input of the next gotree command.

Example:

$ gotree generate binarytree -l 100 -n 10 | gotree stats

This will generate 10 random unrooted binary trees, each having 100 tips, and print statistics about them, for example:

Installation

Binaries

You can download already compiled binaries for the latest release in the release section. Binaries are available for MacOS, Linux, and Windows (32 and 64 bits).

Once downloaded, you can just run the executable without any other downloads.

From sources

In order to compile gotree, you must first download and install Go on your system.

Then you just have to type :

go get github.com/fredericlemoine/gotree/

This will download GoTree sources from github, and all its dependencies.

You can then build it with:

cd $GOPATH/src/github.com/fredericlemoine/gotree/
make

The gotree executable should be located in the $GOPATH/bin folder.

Usage

gotree implements several tree manipulation commands. Here are some short examples:

Generate random unrooted binary trees

$ gotree generate binarytree -l 100 -n 10 | gotree stats

Unrooting a tree

$ gotree unroot -i tree.tre -o unrooted.tre

Unrooting a tree

$ gotree unroot -i tree.tre -o unrooted.tre

Collapsing short branches

$ gotree collapsebrlen -i tree.tre -l 0.001 -o collapsed.tre

Printing statistics of the tree

$ gotree stats -i tree.tre

Printing statistics of the edges

$ gotree stats edges -i tree.tre

Example of result:

Removing tips that are absent from another tree

$ gotree prune -i tree.tre -c other.tre -o pruned.tre

You can test with

$ gotree prune -i <(gotree generate binarytree -l 1000 -n 1) \
               -c <(gotree generate binarytree -l 100 -n 1) \
               | gotree stats

It should print 100 tips.

Comparing bipartitions

Count the number of common/specific bipartitions between two trees.

$ gotree compare -i tree.tre -c other.tre

You can test with random trees (there should be very few common bipartitions)

$ gotree compare -i <(gotree generate binarytree -l 100 -n 1) \
                -c <(gotree generate binarytree -l 100 -n 1)

Renaming tips of the tree

If you have a file containing the mapping between current names and new names of the tips, you can rename the tips:

$ gotree rename -i tree.tre -m mapfile.txt -o newtree.tre

You can try by doing:

$ gotree generate binarytree -l 100 -n 1 -o tree.tre
$ gotree stats tips -i tree.tre | awk '{if(NR>1){print $4 "\tNEWNAME" $4}}' > mapfile.txt
$ gotree rename -i tree.tre -m mapfile.txt | gotree stats tips