A walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calculated. A small CGI site for generating a UPGMA tree from a distance matrix can be found here. The source data for this worked example is a subset of Cytochrome C distances from Table 3 of one of the seminal phylogenetic papers: Fitch WM & Margoliash E (1967). Construction of phylogenetic trees. Science 155:279-84. PowerPoint timings are set up to be consistent with autolooping the presentation.
UPGMA Worked Example
UPGMA Worked Example webpage
http://www.southampton.ac.uk/~re1u06/teaching/upgma/
Related Training Materials
Bioinformatics – the Power of Computers in Biology: A Practical Guide
This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces s …
June 8, 2019
Sequence analysis
A Critical Guide to the neXtProt knowledgebase: querying using SPARQL
This Critical Guide in the Introduction to Bioinformatics series briefly outlines how to e …
June 6, 2019
Database management
Using Bioinformatics to Understand Genetic Diseases: A Practical Guide
This Practical Guide in the Bringing Bioinformatics into the Classroom series outlines a n …
March 18, 2019
A Critical Guide to the PDB
This Critical Guide in the Introduction to Bioinformatics series provides a brief outline …
September 8, 2018
Biological databases, Introduction to the PDB, Protein structure analysisx, Protein structure databases, Protein structures, introduction to bioinformatics
A Critical Guide to InterPro
This Critical Guide in the Introduction to Bioinformatics series provides an introduction …
September 8, 2018
Biological databases, Introduction to InterPro, Protein family classification, Protein family hierarchies, Protein function annotationx, introduction to bioinformatics, protein family databases, protein sequence analysis
A Critical Guide to UniProtKB
This Critical Guide in the Introduction to Bioinformatics series provides a brief outline …
September 8, 2018
Biological databases, Introduction to UniProt, Protein sequence databasesx, The UniProt Knowledgebase, introduction to bioinformatics
A Critical Guide to Unix
This Critical Guide in the Introduction to Bioinformatics series briefly introduces the Un …
September 8, 2018
Biological databases, Introduction to Unix, Operating System, Uni, command linex, commands, introduction to bioinformatics
A Critical Guide to the UniProtKB Flat-file Format
This Critical Guide briefly presents the need for biological databases and for a standard …
September 8, 2018
Biological databases, Flat-file databases, Flat-files, The UniProtKB flat-file formatx, introduction to bioinformatics
A Critical Guide to BLAST
This Critical Guide in the Introduction to Bioinformatics series provides an overview of t …
September 8, 2018
Biological databases, Introduction to BLAST, Sequence database searchingx, Sequence similarity searching, introduction to bioinformatics
Biocuration: An Introduction
Claire O’Donovan, leader of the Protein Function Content team at EMBL-EBI, gives an introd …
May 11, 2018
Biocuration
EMBL-EBI Train Online
If you work in the life sciences, you may find that you’re spending less time doing experi …
May 11, 2018
Chemical biology, Cross-domain, DNA & RNA, Literature, Ontologies, Proteins, Systems, bioinformatics, gene expression, structures
BD2K Data Science Open Educational Resources (OERs)
These Online Educational Resources (OERs) cover a variety of topics related to data scienc …
April 2, 2018
Biocuration, Curation, Identifiers, Ontology, Standards