Overview

NWKIT (/njuːkit/) is a toolkit for manipulating phylogenetic trees in the Newick format.

Installation

The latest version of NWKIT is available from Bioconda. For users requiring a conda installation, please refer to Miniforge for a lightweight conda environment.

Install from Bioconda

conda install bioconda::nwkit

Verify the installation by displaying the available options

nwkit -h

(For advanced users) Install the development version from GitHub

pip install git+https://github.com/kfuku52/nwkit

Optional dependencies for image post-processing

nwkit image can normalize image format, trim margins, and resize/pad output files when the optional image-processing dependencies are installed:

pip install "nwkit[image]"

Subcommands

See Wiki for usage.

• constrain: Generating a species-tree-like Newick file for topological constraint
• collapse: Collapsing internal branches by support and/or branch length
• cladefreq: Summarizing clade frequencies across a tree collection
• consensus: Generating a consensus tree or transferring consensus support to a reference tree
• dist: Calculating topological distance between two trees
• draw: Drawing a phylogenetic tree with optional speciation/duplication node markers
• drop: Removing node and branch information
• image: Retrieving representative species images with license-aware filtering
• info: Printing tree information
• intersection: Dropping non-overlapping leaves/sequences between two trees or between a tree and an alignment
• label: Adding unique node labels
• mark: Adding texts to node labels by identifying the targets with a leaf name regex
• mcmctree: Introducing divergence time constraints for PAML's mcmctree
• monophyly: Assessing whether species or trait-defined groups are monophyletic
• nhx2nwk: Generating Newick from NHX
• nwk2table: Converting a Newick tree into a parent-child table
• printlabel: Searching and printing node labels
• prune: Pruning leaves
• rename: Renaming nodes using a TSV mapping or regular expression
• rescale: Rescale branch length with a given factor
• root: Placing or transferring the tree root
• sanitize: Eliminating non-standard Newick flavors
• shuffle: Shuffling branches and/or labels
• skim: Sampling leaves from clades with shared traits
• subtree: Generating a subtree Newick file
• table2nwk: Converting a parent-child table into a Newick tree
• transfer: Transferring information between trees
• validate: Validating one or more Newick trees and reporting structural issues

Citation

There is no published paper on NWKIT itself, but we used and cited NWKIT in several papers including Fukushima & Pollock (2023, Nat Ecol Evol 7: 155-170).

Licensing

This program is MIT-licensed. See LICENSE for details.