The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell

By Thomas Junier, E. Zdobnov. Bioinform., 2010

715 citations recorded by the source corpus.

Summary: We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes. Availability: C source code, Python bindings and executables for various platforms are available from http://cegg.unige.ch/newick_utils. The distribution includes a manual and example data. The package is distributed under the BSD License. Contact: thomas.junier@unige.ch

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/e7b4e7bcc533c7f6fb49a06c20e5d9cc9c21db9b

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Plant Science

Citations in the corpus

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees (2018, methodology): “To address RQ1, we draw bootstrap support values on the ML gene trees and then contract branches with bootstrap support up to a threshold (0, 3, 5, 7, 10, 20, 33, 50, and 75%,) using the newick utility package [45].”
Trimmomatic: a flexible trimmer for Illumina sequence data (2014, methodology): “In other domains, this can be achieved using a shell pipeline to combine multiple tools as required, e.g. in Newick (Junier and Zdobnov, 2010).”