Exercises

1. The Tree of Life

View a random page at the Tree of Life. Search for Proboscidae, Decapodiformes, and anteater.

2. Draw a tree with the following sequences

HGLCS
HALCS
HAICS
PAICS
PAICT

3. What's Going On Here?

Run a BLAST search with n-Acetylneuraminate lyase V. cholerae
Choose appropriate accession numbers or use this Accession File
Get the sequences via Batch Entrez or use these Sequences. Here are the Edited Sequences
Create a multiple alignment using ClustalW at at PISE or at EBI (Clustal format; Phylip format). You could also run Boxshade on the ClustalW output (results)
Create a tree using protpars (results). You can create a phenogram and a tree.
Submit the ClustalW file to protdist to create a distance matrix (results), which can be submitted to neighbor (NJ and UPGMA trees; NJ & UPGMA), fitch (resuts, clock results), and kitsch (results)
Create a consensus tree at WebPHYLIP (results)
Submit the ClustalW file to BAMBE
Can you submit the Clustal file to LVB?

4. More Weird Evolution

5. Another Mammoth Undertaking

6. How many species?

fastDNAml creates maximum likelihood trees for DNA sequences

7. What the Heck is a Parti-Coloured Bear?

Find out the more common name for this animal
WITHOUT using the Taxonomy Browser, find out some animals that might be related to this and get appropriate sequences
Conduct the appropriate phylogenetic analysis

8. Align Everything

Murphy et al. Molecular Phylogenetics of Placental Mammals

BLOSUM 62 Matrix in Word | Plain Text | Excel format
n-Acetylneuraminate lyase V. cholerae | Accession File | Sequences | Edited Sequences
Hyaluron Synthase Accession File | Sequences