gotree

README

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 uniformtree -l 100 -n 10 | gotree stats

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

tree	nodes	tips	edges	meanbrlen	meansupport	mediansupport	rooted
0	198	100	197	0.0821	-1.0000	-1.0000	unrooted
1	198	100	197	0.0898	-1.0000	-1.0000	unrooted
2	198	100	197	0.0765	-1.0000	-1.0000	unrooted
3	198	100	197	0.0746	-1.0000	-1.0000	unrooted
4	198	100	197	0.0846	-1.0000	-1.0000	unrooted
5	198	100	197	0.0784	-1.0000	-1.0000	unrooted
6	198	100	197	0.0884	-1.0000	-1.0000	unrooted
7	198	100	197	0.0943	-1.0000	-1.0000	unrooted
8	198	100	197	0.0885	-1.0000	-1.0000	unrooted
9	198	100	197	0.0839	-1.0000	-1.0000	unrooted

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 uniform binary trees

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

Unrooting a tree

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

Collapsing short branches

$ gotree collapse length -i tree.tre -l 0.001 -o collapsed.tre

Collapsing lowly supported branches

$ gotree collapse support -i tree.tre -s 0.8 -o collapsed.tre

Clearing length information

$ gotree clear lengths -i tree.nw -o nolength.nw

Clearing support information

$ gotree clear supports -i tree.nw -o nosupport.nw

Note that you can pipe the two previous commands:

$ gotree clear supports -i tree.nw | gotree clear lengths -o nosupport.nw

Printing tree statistics

$ gotree stats -i tree.tre

Printing edge statistics

$ gotree stats edges -i tree.tre

Example of result:

tree	brid	length	support	terminal	depth	topodepth	rightname
0	0	0.107614	N/A	false	1	6
0	1	0.149560	N/A	true	0	1	Tip51
0	2	0.051126	N/A	false	1	5
0	3	0.003992	N/A	false	1	4
0	4	0.030974	N/A	false	1	3
0	5	0.270017	N/A	true	0	1	Tip84
0	6	0.029931	N/A	false	1	2
0	7	0.001136	N/A	true	0	1	Tip70
0	8	0.011658	N/A	true	0	1	Tip45
0	9	0.104188	N/A	true	0	1	Tip34
0	10	0.003361	N/A	true	0	1	Tip16
0	11	0.021988	N/A	true	0	1	Node0

Printing tips

$ gotree stats tips -i tree.tre

Example of result:

tree	id	nneigh	name
0	1	1	Tip8
0	2	1	Node0
0	5	1	Tip4
0	8	1	Tip9
0	9	1	Tip7
0	11	1	Tip6
0	13	1	Tip5
0	14	1	Tip3
0	16	1	Tip2
0	17	1	Tip1

Comparing tips of two trees

$ gotree compare tips -i tree.tre -c tree2.tre

This will compare the two sets of tips.

Example:

$ gotree compare tips -i <(gotree generate uniformtree -l 10 -n 1) \
                      -c <(gotree generate uniformtree -l 11 -n 1)
> Tip10
= 10

10 tips are equal, and "Tip10" is present only in the second tree.

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 uniformtree -l 1000 -n 1) \
               -c <(gotree generate uniformtree -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 trees -i tree.tre -c other.tre

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

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

Tree	specref	common
0	97	0

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 uniformtree -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