What we expect you to know
You should know, what these terms mean and you should be able to explain them in your own words.
similarity matrix . molecular clock . 18S RNA . internally transcribed spacer . haplotype . universal primer . African Eve . alignment . gaps . discrete and distance based algorithms . Maximum Parsimony . Neighbour Joining . Maximum Likelihood . UPGMA . transition and transversion . bootstrap value . outgroup . root of a tree . genetic barcoding . taxon gap
03 Molecular Phylogeny: Exercise
You have to construct a phylogenetic tree for a taxonomic group of your choice based on the genetic barcoding marker rbcL. Perform the following steps:
- get the sequences for the genus from the NCBI database
- generate an alignment
- construct a phylogenetic tree based on NJ (with bootstrap values).
Instructions, how to handle sequence data you find here (unpublished material, therefore protected by password)