biology

Treefinder

Treefinder 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 Treefinder rather than just read about it. In short: Treefinder is a computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences. It was written by Gangolf Jobb, a former researcher at LMU Munich, Germany, and was originally released in 2004.

Key takeaways

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

Reference excerpt

Treefinder is a computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences. It was written by Gangolf Jobb, a former researcher at LMU Munich, Germany, and was originally released in 2004. Treefinder is free of charge, though the most recent license prohibits its use in the USA and eight European countries.

Overview A platform-independent graphical environment integrates a standard suite of analyses: phylogeny reconstruction, bootstrap analysis, model selection, hypothesis testing, tree calibration, manipulation of trees and sequence data. Treefinder is scriptable through a proprietary scripting language called TL. Treefinder has an efficient tree search algorithm that can infer trees with thousands of species within a short time. Result trees are displayed and can then be saved as a reconstruction report, which may serve as an input for further analysis, for example hypothesis testing. The report contains all information about the tree and the models used. Treefinder also supports exporting results as NEWICK or NEXUS files. The software supports a broad collection of models of sequence evolution. The June 2008 release implements 7 models of nucleotide substitution (HKY, TN, J1, J2, J3 (= TIM), TVM, GTR), 14 empirical models of amino acid substitution (BLOSUM, cpREV, Dayhoff, JTT, LG, mtArt, mtMam, mtREV, PMB, rtREV, betHIV, witHIV, VT, WAG), 4 substitution models of structured rRNA (bactRNA, eukRNA, euk23RNA, mitoRNA), the 6-state "Dayhoff Groups" protein model (DG), 2-state and 3-state models of DNA (GTR3, GTR2), a parametric mixed model (MIX) mixing the empirical models of proteins or rRNA, and also a user-definable GTR-type model (MAP) mapping characters to states as needed. Three models of among-site rate heterogeneity are available (Gamma, Gamma+I, I), which can be combined with any of the substitution models. One can assume different models for different partitions of a sequence alignment, and partitions may be assumed to evolve at different speeds. All parameters of the models can be estimated from the data by maximization of likelihood. Certain TL expressions, the "model expressions", allow the concise notation of complex models, together with their parameters and optimization modes. As of November 2015, Treefinder's original publication from 2004 has been cited more than 700 times in the scientific literature.

Controversy On February 1, 2015, Jobb disallowed the use of Treefinder in the USA in order to make a political statement. The author again changed the license terms on October 1, 2015 to exclude use in Germany, Austria, France, the Netherlands, Belgium, Great Britain, Sweden, and Denmark - countries he claimed "host most of the non-european immigrants". In an accompanying statement, he decried the handling of the European migrant crisis by European countries. The journal BMC Evolutionary Biology that published the original application note has since retracted it, stating that the license change violated the journal's policy.

See also Computational phylogenetics Molecular phylogeny

References

External links Treefinder homepage

Worked examples

Example 1 — a first encounter with Treefinder

Start with the simplest possible case. Write down what Treefinder 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 Treefinder 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 Treefinder 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 Treefinder

In research: Treefinder 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 Treefinder 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: Treefinder 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 Treefinder 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 Treefinder in 20 minutes

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

Frequently asked questions

What is Treefinder in simple terms?

Why does Treefinder 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 Treefinder?

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 Treefinder.