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Updated: Mar 7, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Phyx: phylogenetic tools for unix.

Joseph W Brown¹, Joseph F Walker¹, Stephen A Smith¹

¹Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.

Bioinformatics (Oxford, England)

|February 9, 2017

Summary

This summary is machine-generated.

Phylogenetic analysis is computationally intensive. The phyx software suite, using C++ and Unix-like tools, offers efficient processing of large phylogenomic datasets by minimizing memory usage.

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Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Generating phylogenomic data has increased computational demands for phylogenetic studies.
Existing tools may struggle with the scale of modern datasets.

Purpose of the Study:

To present phyx, a software collection for phylogenetic object manipulation and analysis.
To provide efficient computational solutions for large-scale phylogenetics.

Main Methods:

phyx is a collection of C++ programs designed for phylogenetic objects (alignments, trees, MCMC logs).
It utilizes a Unix/GNU/Linux command-line tool paradigm, with individual programs performing single tasks.
Standard input/output streams allow for the creation of complex analytical pipelines.

Main Results:

phyx minimizes memory requirements by processing data in a stream-centric manner.
This approach enables efficient handling of very large phylogenetic datasets.

Conclusions:

phyx addresses the escalating computational burden in phylogenetics.
The software facilitates exploration, manipulation, analysis, and simulation of phylogenetic data efficiently.