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## A friend to tend to your trees
PhyloBuddy is intended to assist in the management and manipulation of phylogenetic trees and as a wrapper for common phylogenetic inference programs. Currently supported formats are [Newick](https://en.wikipedia.org/wiki/Newick_format), [NEXUS](https://en.wikipedia.org/wiki/Nexus_file), and [NeXML](http://www.nexml.org/).
Command line sequence manipulation tools
Function Flag Parameters Brief Description
consensus_tree -ct
[min frequency (float)]
Generate a consensus tree (default 0.5)
display_trees -dt
None
Visualize trees graphically
distance -cd
[{'wrf'|'uwrf'|'ed'}]
Calculates tree distance using weighted/unweighted Robinson-Foulds, or euclidean distance (default wrf)
generate_tree -gt
[{'raxml' | 'phyml' | 'fasttree'}, <tool specific parameters>]
Accept alignment file as input, and perform phylogenetic inference with a third party program
hash_ids -hi
[hash length (int)]
Rename all identifiers to random hashes
list_ids -li
[num columns (int)]
Output all taxa/leaf identifiers in columns (default 1 column)
print_trees -ptr
None
Prints an ASCII representation of each tree.
prune_taxa -pt
<regex, [regex, ...]>
Remove taxa with matching labels/IDs
rename_ids -ri
<regex> <substitution>
Replace matched regular expressions in ids with new text
root -rt
[taxa, [taxa, ...]]
(Re)root a tree at its midpoint or on specified taxa
screw_formats -sf
<out format>
Change the format of a tree file
show_unique -su
None
Color leaf branches based on whether the taxa is present in both trees
split_polytomies -sp
None
Randomly resolves polytomies
unroot -ur
None
Make trees unrooted
Flag Brief Description
-f --format
Force read a specific tree format (very rarely necessary)
-i --in_place
Rewrites the FIRST input file with the final output. Be careful!
-k --keep_temp
Specify a directory to send temporary files to (if any)
-o --out_format
Specify the format you want the output returned in.
-q --quiet
Suppress stderr messages.
-t --test
Run the function and return any stderr/stdout other than the alignment
