Download Plasmodium falciparum causes malaria in humans

Phylogenetics Homework Assignment
(Remember that ‘Ctrl-PrintScreen’ will capture the image on a screen to the computer’s clipboard which
can then be pasted into an image editing program like Photoshop to be manipulated for use in your
homework. Alternatively the alignments and trees can be printed out separately.)
Perform a BLAST using the sequence provided, retrieve all of the initial
matching sequences. With the best alignment of these sequences, estimate
the phylogenetic relationships between these sequences.
1. Show the alignment and the resulting tree including taxonomic units
(species names).
2. List point by point (place each new point on a new line) what you can and
can’t learn from this tree and what could be done to improve it.
3. Implement those improvements. Create an alignment of related
sequences that will result in a tree with good support that describes the
diversity of this protein across a range of different organisms. Show the
alignment used for phylogenetic estimation and the resulting tree.
4. If I were interested in the pathway of which this protein is a part, and
asked for advice on increasing the resolution of the phylogenetic estimates,
what advice would you give on how to proceed? List point by point (on new
lines as aabove).
5. Take the advice given in the previous question and present your ‘ultimate’
phylogenetic analysis of the pathway this protein is involved in.
6. I’m interested in therapies against malaria. Does your analysis provide
me with any useful information? If so, what? How could that information be
used?