PhyloBuddy
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, NEXUS, and NeXML.
$: pb file(s) <tool> <args> <modifier(s)>
pb: Alias for phylobuddy used throughout the wiki (see Creating Aliases)
file(s): One or more tree files in any combination of NEXUS, Newick, and NeXML formats. Note that the files argument must be left blank if piping data into PhyloBuddy.
tool: A single flag that specifies which PhyloBuddy tool is being run. All tools are listed in the table below.
args: If the tool being called accepts any additional arguments, they must be supplied here. All arguments are explained in detail in each tool's wiki page.
modifier(s): These are additional flags that may be passed into PhyloBuddy to modify general behavior, irrespective of the tool being called. All modifiers are listed in the table below.
| Tool | Flag | Parameters | Brief Description |
|---|---|---|---|
| add_branch | -ab | <branch/subtree> <sister, [sister, ...]> | Add a new branch to an existing tree |
| collapse_polytomies | -cpt | [threshold (float)] [{'bootstrap' | 'length'}] | Remove nodes if their support value or branch length are below a threshold |
| consensus_tree | -ct | [min frequency (float)] | Generate a consensus tree (default 0.5) |
| display_trees | -dt | None | Visualize trees graphically |
| distance | -dis | [{'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 |
| ladderize | -ld | ['rev'] | Sort all nodes by their number of children |
| list_ids | -li | [num columns (int)] | Output all taxa/leaf identifiers in columns (default 1 column) |
| num_tips | -nt | None | Display the number of tips in each tree |
| 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 store any temporary files produced during execution. |
| -o --out_format | Specify the supported format you want the output returned in. |
| -q --quiet | Suppress stderr messages. |
| -s --random_seed | Specify a random seed |
| -t --test | Run the function and return any stderr/stdout other than the alignment. |
