Budgitree newick tree processor
Project description
Budgitree
Why use this program?
Let's say you have just obtained your phylogenetic tree from FastTree.
This tree will likely contain polytomies, and branch lengths that are so
small that they will be represented in exponential notation.
Some programs will not accept trees with these two features (e.g., ClusterPicker).
You could remove the polytomies with the ape
package in R
. But how do you
print the tree to standard out with the branch lengths in standard float format? You could submit
an issue to the developers of your target program and hope they respond with a fix.
Both of these options may delay your workflow. This program provides a python3 solution
to your problems. Given a phylogenetic tree in newick format, budgitree
provides an easy way to print your tree to stdout
with:
- Polytomies resolved (i.e., tree converted to strictly bifurcating) and/or
- Exponential notation removed (i.e., branch lengths in float format with user-specified number of decimal places
- Collapse branches with support values less than the specified cutoff (default is do nothing)
Usage
Get help
$ budgitree
usage: budgitree [-h] ...
Given a newick tree, use this program to resolve polytomies (convert to
bifurcating) and or change the formatting of branch lengths.
optional arguments:
-h, --help show this help message and exit
Sub-commands help:
smuggle Smuggle the budgies.
version Print version.
test Run test suite.
Start smuggling
$ budgitree smuggle -h
usage: budgitree smuggle [-h] [-p PRECISION] [-b] [-c COLLAPSE] tree
Process the tree.
positional arguments:
tree Input newick tree
optional arguments:
-h, --help show this help message and exit
-p PRECISION, --precision PRECISION
Branch length precision (i.e., number of decimal
places to print).
-b, --dont_bifurcate_polytomies
Switch off conversion of node polytomies to
bifurcating
-c COLLAPSE, --collapse COLLAPSE
Collapse nodes with support values less than this.
Installation
pip3 install git+https://github.com/schultzm/Budgitree.git
Testing
budgitree test
Project details
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