biology

HYPHY

HYPHY is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand HYPHY rather than just read about it. In short: HYPHY ( HY-fy) is a free multiplatform (Mac, Windows and UNIX) computational phylogenetics software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies".

Key takeaways

HYPHY belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect HYPHY to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of HYPHY from memory before moving on to harder problems.

Reference excerpt

HYPHY ( HY-fy) is a free multiplatform (Mac, Windows and UNIX) computational phylogenetics software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies". As of March 2018, about 2,000 peer-reviewed scientific journal articles cite HYPHY.

Major features HYPHY supports analysis of nucleotide, protein and codon sequences, using predefined standard models or user-defined models of evolution. The package supports interaction through a graphical user interface as well as a batch language to set up large and complicated analyses and process the results. HyPhy includes a versatile suite of methods to detect adaptive evolution at individual amino-acid sites and/or lineages, including generalizations of Nielsen-Yang PAML and Suzuki-Gojobori approaches and many others.

History The development of HyPhy started in 1997, with the first public release in 2000 and the most recent version as of December 2020 being 2.5.

Software/code availability and license HYPHY is distributed as freeware with source code released under the MIT License. Compiled binaries for Mac OS X and Windows are available for download. The source code is available so that users can compile the HyPhy application on POSIX systems. A subset of HYPHY methods for detecting adaptive evolution are also made available by the HYPHY team at Temple University on the DataMonkey cluster.

Notes

External links [1]: The HYPHY home page [2]: The DataMonkey server, which supports a variety of HYPHY tools (at no cost). [3]: HYPHY/DataMonkey support

Worked examples

Example 1 — a first encounter with HYPHY

Start with the simplest possible case. Write down what HYPHY claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to HYPHY before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about HYPHY ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of HYPHY

In research: HYPHY appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses HYPHY in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: HYPHY is common in secondary-school and first-year university syllabi. It links to neighbouring topics Phylogenetics software, so understanding it makes those chapters shorter.
In everyday life: Look for HYPHY outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study HYPHY in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what HYPHY means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain HYPHY out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is HYPHY in simple terms?

Why does HYPHY matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study HYPHY?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on HYPHY.