The general command line for running jclusterfunk is:
jclusterfunk <command> [options]
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
-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.
-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 |
)
--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).
-k
--keep-taxa
Keep the taxa specifed (default: prune specified taxa)
--decreasing
Order nodes by decreasing clade size.
--increasing
Order nodes by increasing clade size.
--outgroup <outgroup taxa>
Root tree using specified outgroup
--midpoint
Root tree at the branch-length midpoint.
--attribute <attribute>
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