Gotree is a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language.
Gotree handles phylogenetic trees in Newick, Nexus, PhyloXML and Nextstrain/Augur v2 format, through several basic commands. Each command may print result (a tree for example) in the standard output, and thus can be piped to the standard input of the next gotree command.
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.
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/evolbioinfo/gotree/This will download GoTree sources from github, and all its dependencies.
You can then build it with:
cd $GOPATH/src/github.com/evolbioinfo/gotree/
makeThe gotree executable should be located in the $GOPATH/bin folder.
Here is the list of all commands, with the link to the full description, and a link to a snippet that does it in GO.
| Command | Subcommand | Description |
|---|---|---|
| annotate (api) | Annotates internal nodes of a tree with given data | |
| brlen (api) | Modifies branch lengths | |
| -- | clear | Clear lengths from input trees |
| -- | cut | Cut branches whose length is greater than or equal to the given length |
| -- | round | Rounds branch lengths from input trees with a given precision |
| -- | scale | Scales branch lengths from input trees by a given factor |
| -- | setmin | Sets a min branch length to all branches with length < cutoff |
| -- | setrand | Assigns a random length to edges of input trees |
| -- | set | Assigns a given length to edges of input trees |
| collapse (api) | Collapses/Removes branches of input trees | |
| -- | clade | Collapses a clade and replace it ith a tip |
| -- | depth | Collapses/Removes branches of input trees having a given depth |
| -- | length | Collapses/Removes short branches of input trees |
| -- | single | Collapses/Removes branches that connect single internal nodes (linear paths) |
| -- | support | Collapses/Removes lowly supported branches of input trees |
| comment (api) | Modifies branch/node comments | |
| -- | clear | Clears branch/node comments from input trees |
| -- | transfer | Transfers node names to comments |
| compare (api) | Compares full trees, edges, or tips | |
| -- | edges | Individually compares edges of the reference tree to a compared tree |
| -- | tips | Compares the set of tips of the reference tree to a compared tree |
| -- | trees | Compare 2 trees in terms of common and specific branches |
| completion | Generates auto-completion commands for bash or zsh | |
| compute (api) | Computations such as consensus and supports | |
| -- | bipartitiontree | Builds one tree with only one given bipartition |
| -- | consensus | Computes the consensus from a set of input trees |
| -- | edgetrees | Writes one output tree per branch of the input tree, with only one branch |
| -- | support classical | Computes classical bootstrap supports |
| -- | support booster | Computes booster bootstrap supports |
| divide | Divides an input tree file into several tree files | |
| download (api) | Downloads trees from a server | |
| -- | itol | Downloads a tree image from iTOL, with given image options |
| -- | ncbitax | Downloads the full ncbi taxonomy from NCBI ftp server and cinverts it in Newick |
| -- | panther | Downloads a tree from Panther database (http://pantherdb.org/) |
| draw (api) | Draws tree(s) with different layouts | |
| -- | text | Draws tree(s) in text/ascii format |
| -- | png | Draws tree(s) in png format |
| -- | svg | Draws tree(s) in svg format |
| -- | cyjs | Draws tree(s) in a html file, using cytoscape js |
| generate (api) | Generates random trees, branch lengths are simply drawn from an expontential(0.1) law | |
| -- | balancedtree | Randomly generates perfectly balanced trees |
| -- | caterpillartree | Randomly generates perfectly caterpillar trees |
| -- | startree | Generates a star tree (no internal branches) |
| -- | topologies | Generates all possible tree topologies |
| -- | uniformtree | Randomly generates uniform trees |
| -- | yuletree | Randomly generates Yule-Harding trees |
| graft (api) | Graft a tree on an input tree | |
| labels | Lists labels of tree tips | |
| ltt | Draws a lineage through time plot | |
| matrix (api) | Prints distance matrix associated to the input tree | |
| merge (api) | Merges two rooted trees | |
| nni (api) | Generates all NNI neighbors from a given tree | |
| prune (api) | Removes tips of input trees | |
| reformat (api) | Reformats input file | |
| -- | newick | Reformats input file (nexus, newick, phyloxml) into newick |
| -- | nexus | Reformats input file (nexus, newick, phyloxml) into nexus |
| -- | phyloxml | Reformats input file (nexus, newick, phyloxml) into phyloxml |
| rename (api) | Renames tips/nodes of the input tree | |
| repopulate (api) | Re populate the tree with identical tips (having the exact same sequence) | |
| reroot (api) | Reroots trees using an outgroup or at midpoint | |
| -- | midpoint | Reroots trees at midpoint position |
| -- | outgroup | Reroots trees using a given outgroup |
| rotate (api) | Reorders neighbors of internal nodes. Does not change the topology, but just traversal order. | |
| -- | sort | Sort neighbors of internal nodes by ascending number of tips |
| -- | rand | Randomly reorders neighbors of internal nodes |
| resolve (api) | Resolves multifurcations by adding 0 length branches | |
| -- | named | Resolves internal named nodes as new tips with 0 length branches |
| sample | Samples trees from a set of input trees | |
| shuffletips (api) | Shuffles tip names of an input tree | |
| subtree (api) | Extracts a subtree starting at a given node | |
| support (api) | Modifies branch supports | |
| -- | clear | Clears branch supports from input trees |
| -- | round | Rounds branch supports from input trees with a given precision |
| -- | scale | Scales branch supports from input trees by a given factor |
| -- | setrand | Assigns a random support to edges of input trees |
| stats (api) | Prints statistics about the tree, its edges, its nodes, if it is rooted, and its tips | |
| -- | edges | Prints informations about all the edges |
| -- | monophyletic | Tells wether input tips form a monophyletic group in input trees |
| -- | nodes | Prints informations about all the nodes |
| -- | rooted | Tells if the tree is rooted or not |
| -- | tips | Prints informations about all the tips |
| -- | splits | Prints all the splits/bipartitions of the tree (bit vectors) |
| unroot (api) | Unroots input tree(s) | |
| upload (api) | Uploads trees to a given server | |
| -- | itol | Uploads trees to itol, with given annotations |
| version | Prints gotree version |