jclusterfunk

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The general command line for running jclusterfunk is:

jclusterfunk <command> [options]

commands

command	description
annotate	Take data fields from a metadata file and apply either to the tip labels of the tree or as annotations as used by FigTree.
cluster	Finds and annotates monophyletic clusters of taxa have the specified annotation value. The cluster number is an incrementing value.
collapse	Collapses branches less than a threshold into a polytomy.
context	Extracts subtrees that are close ancestors, siblings or children of a set of tip.
convert	Convert the tree from one format to another without changing it.
divide	Divides up a tree into roughly equal sized subtrees.
extract	Extracts metadata fields from the tips of a tree.
insert	Replaces a tip in a tree with a polytomy of specified taxa.
merge	Merges two metadata tables based on an index column (usually taxon names).
prune	Prune out sets of tips from a tree.
Reconstructs	Reconstructs annotation values at internal nodes using parsimony.
reorder	Reorder branches at each node to have increasing or decreasing numbers of child nodes.
reroot	Reroot the tree using an outgroup or at the midpoint.
sample	Sample taxa down using metadata attributes.
scale	Scales branch lengths of a tree by a factor or to a specified root height.
split	Split the tree into subtrees defined by annotations of the tips or the nodes.
statistics	Writes out a list of statistics and information about a tree.
tmrca	Finds the time of most recent common ancestor of a set of taxa.

annotate assign cluster collapse extract subcluster conquer context convert divide insert merge prune reconstruct reorder reroot sample scale split statistics tmrca

general options

-h / --help List the available options and stop. Combine with a command to get help for that command.

--version Print the version number and stop.

-v / --verbose Print extended information about analysis performed.

-i / --input <filename> Specify the input tree file.

-m / --metadata <filename> Specify a metadata table in CSV format where required.

-t / --taxa <filename> Specify a list of taxa in CSV format or as a tree where required.

-o / --output <output_path> Output filename or path to a directory if multiple output files will be produced.

-f / --format <nexus|newick> Output tree file format (nexus or newick)

-p / --prefix <file_prefix> Output file prefix when multiple output files are produced.

taxa matching options

-c / --index-column <column name> Metadata column to use to match tip labels (default first column)

--index-field <field number> The tip label field to use to match metadata rows indexed from 1 (default = whole label)

--field-delimiter <delimiter> The delimiter used to specify fields in the tip labels (default |)

command specific options

annotate

--label-fields <columns> A list of metadata columns to add as tip label header fields.

--tip-attributes <columns> A list of metadata columns to add as tip attributes.

--ignore-missing Ignore any tips that don’t have a match in the annotations table (default: stop and report missing metadata).

--replace Replace the existing annotations or tip labels rather than appending (default: append).

context

prune

-k --keep-taxa Keep the taxa specifed (default: prune specified taxa)

reorder

--decreasing Order nodes by decreasing clade size. --increasing Order nodes by increasing clade size.

reroot

--outgroup <outgroup taxa> Root tree using specified outgroup --midpoint Root tree at the branch-length midpoint.

split

--attribute <attribute>

Installation

The easiest way to install is using conda:

conda install cov-ert::jclusterfunk

Alternatively, the download the latest binary: https://github.com/cov-ert/jclusterfunk/releases/latest

This contains two files: jclusterfunk an executable shell file jclusterfunk.jar the Java jar file

Both of these can be copies to a bin directory on the path such as /usr/local/bin or ~/bin