A tiny package that implements the TimeTree type for representing
fully-resolved phylogenetic time trees in Julia. A constructor which generates
TimeTrees from Newick strings is provided, as are methods for manipulating
existing trees. In addition, a plot method is implemented which generates an
ASCII depiction of a tree.
Here's an example of a TimeTree being generated from its Newick representation and an ASCII visualization displayed in an interactive Julia session:
julia> using TimeTrees
julia> t = TimeTree(newick)
julia> plot(t)
/----------------------* 1
/-------------------------------+----------------------* 2
| /----------------------------* 3
/-------------+ /+ /-------------------* 4
| | |\--------+ /-* 5
| \------------------------+ \-----------------+-* 6
| | /---------* 7
| | /---+---------* 8
| \---------------+/------------* 9
+ \+ /* 10
| \-----------+* 11
| \* 12
| /------------------------------* 13
| /------------------------------+ /--------------+-----------* 14
| | | | \-----------* 15
| | \---+ /--------------+* 16
\------+ \----------+ \* 17
| \---------------* 18
| /-* 19
\-----------------------------------------------------------+-* 20
(Assuming that the variable newick holds a string containing the Newick
representation.)
Trees with non-contemporaneous leaf ages are also supported:
julia> plot(t, labelLeaves = false)
/-------*
/-------------------+-----------------------------------------------*
| /-----------------------------------------*
+ | /--------------------*
| | /-------------------+ /---------*
\---+ | \----+---------------+---*
| | \---------*
| | /-------------*
\------+-----------------------+ *
| \--------+ /-+----*
| | | \------*
| \----+-----------+-*
+ \------*
| /-----------------------------------------*
| /---------+ /--------------*
| | \-----+--------------------------------*
\-----+ /--------------------------*
\------------+----------+----------*
| /-------*
\----------------------------+---------*
TimeTrees is not yet a registered Julia package, so you'll need to install it directly from the Github repository:
Pkg.clone("http://github.com/tgvaughan/TimeTrees.jl")
Documentation is available through Julia's built-in help system. To get started, enter the following once the package is installed:
using TimeTrees
?TimeTrees
For license information, see the LICENSE.md file in this directory.