Introduction to Molecular Phylogenetics (DAY 2)

This will introduce undergraduate students to some simple bioinformatics tools that are used to build phylogenetic trees. This isn't an exhaustive exploration of all the tools that exist. Nor is it designed to cover all the different phylogenetic tree building methods. It is simply designed to expose students to acquiring sequence data and building phylogenetic trees.


Documents


Example Sequences for Presentation


Unknown sequence for Lab


Sequences for homework problem 1

Sequences for homework problem 2

Sequences for homework problem 3

 

 

 

 

 

Bioinformatics websites

Links to Bioinformatics resources.

  • NCBI homepage - A resource for bioinformatics tools and databases
  • Align - Pairwise alignment tool at EBI
  • BLAST - BLAST at NCBI
  • ClustalW - Multiple sequence alignment tool and phylogenetic tree building tool at EBI
  • Dialign - Multiple sequence alignment tool
  • Tcoffee - A rigorous multiple sequence alignment tool
  • Combine - Tool that combines multiple sequence alignments
  • Phylodendron - Phylogenetic Tree drawing program
  • ExPASy homepage - A resource for bioinformatics tools and protein databases
  • EBI homepage - A resource for bioinformatics tools and protein databases
  • Phylip - Online phylogenetic tree building tool

Link to Molecular Evolutionary Genetics Analysis (MEGA) software

  • MEGA - FREE Phylogenetics Analysis Program