Package: budgitree
BudgitreeWhy 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 theapepackage inR.  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,budgitreeprovides an easy way to print your tree tostdoutwith:Polytomies resolved (i.e., tree converted to strictly bifurcating) and/orExponential 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)UsageGet 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 budgie.
    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.Collapse branchesCollapse branches with less than 0.5 support:budgitree smuggle treefile.tre -c 0.50`Print tree with branch supports to 20 decimal places (remove exponential notation):budgitree smuggle treefile.tre -p 20Stop removal of polytomies during run:If for some reason you would like to retain the polytomies, switch the feature off:budgitree smuggle treefile.tre -bCombine the optionsRemove polytomies, print branch lengths to 15 decimal places, collapse nodes <0.5:budgitree smuggle treefile.tre -p 15 -c 0.5InstallationUsingpip:pip3 install budgitreeThe development version:pip3 install git+https://github.com/schultzm/Budgitree.gitTestingRun the test suite to check the software works as intended:budgitree testVersionPrint the version to stdout:budgitree versionEtymologyThe budgerigar, or "budgie", is an Australian bird (Melopsittacus undulatus), keeping
with an Australian theme after @tseemann.  The software sets digits on branches – if you
are imaginative, that kind of sounds likebudgit.treeis because it operates on
phylogenetic trees.  Thesmugglefeature ofbudgitreehas to do with an Australian
joke involving budgie and swimwear.