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Phylogeny Tasks

Task 10.5

Describe various methods of phylogenetic tree analysis.

Task 10.6

You want to build an HIV pedigree on HIV-1 polymerase, how do you go about it?

Task 10.7

How would you construct a phylogenetic tree for RNA polymerase II?

Task 10.8

Calculate a phylogenetic tree using CLUSTAL and MUSCLE. What are the similarities/

differences?

Task 10.9

What is multiple alignment and what can I use it for?

Task 10.10

Familiarize yourself with the SMART/Pfam database and look at a domain family/seed

alignment using an example of your own choosing.

Useful Tools and Web Links

UniProt

https://www.uniprot.org/

InterPro

https://www.ebi.ac.uk/interpro/

Pfam

https://pfam.xfam.org/

SMART

https://smart.embl-­heidelberg.de/

ELM

https://elm.eu.org/

ITS2

https://its2.bioapps.biozentrum.uni-­wuerzburg.de/

Literature

Adamala K, Engelhart AE, Szostak JW (2015) Generation of functional RNAs from inactive oli­

gonucleotide complexes by non-enzymatic primer extension. J Am Chem Soc 137(1):483–489

Bhardwaj G, Mulligan VK, Bahl CD et al (2016) Accurate de novo design of hyperstable con­

strained peptides. Nature 538(7625):329–335. https://doi.org/10.1038/nature19791. (PubMed

PMID: 27626386)

Brito IL, Yilmaz S, Huang K et al (2016) Mobile genes in the human microbiome are structured from

global to individual scales. Nature 535(7612):435–439. (PubMed PMID: 27409808; PubMed

Central PMCID: PMC4983458)

10  Understand Evolution Better Applying the Computer