biology

PAUP*

PAUP* 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 PAUP* rather than just read about it. In short: PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford.

Key takeaways

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

Reference excerpt

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implemented parsimony, but from version 4.0 (when the program became known as PAUP*) it also supports distance matrix and likelihood methods. Version 3.0 ran on Macintosh computers and supported a rich, user-friendly graphical interface. Together with the program MacClade, with which it shares the NEXUS data format, PAUP* was the phylogenetic software of choice for many phylogenetists. Version 4.0 added support for Windows (graphical shell and command line) and Unix (command line only) platforms. However, the graphical user interface for the Macintosh does not support versions of Mac OS X higher than 10.14 (although a GUI for later versions of Mac OS is planned). PAUP* is also available as a plugin for Geneious. PAUP*, which now sports the self-referential title of PAUP* (* Phylogenetic Analysis Using PAUP), is undergoing rapid updates and it now includes the "species tree" method SVDquartets, in addition to parsimony, likelihood, and distance methods for phylogenetics.

References

External links Official website Official test version website

Worked examples

Example 1 — a first encounter with PAUP*

Start with the simplest possible case. Write down what PAUP* 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 PAUP* 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 PAUP* 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 PAUP*

In research: PAUP* 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 PAUP* 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: PAUP* 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 PAUP* 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.

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How to study PAUP* in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what PAUP* 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 PAUP* out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is PAUP* in simple terms?

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford.

Why does PAUP* 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 PAUP*?

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 PAUP*.