Bootstrapping. Due Wednesday, April 25th. Hand it in and be prepared to briefly share your findings with the class.

Groups:

• Group 1: Amanda, Bethany, Eric, Maria.
  Species: Homo sapiens, Mus musculus, Canis familiaris, Felis catus, Ursus maritimus.


• Group 2: Brad, Luke, Marissa, Terry.
  Species: Sus scrofa, Bos taurus, Physeter catodon, Homo sapiens, Ovis aries.


• Group 3: Shane, Noland, Alayna, Doug.
  Species: Tetraodon nigroviridis, Homo sapiens, Xenopus laevis, Gallus gallus, Strongylocentrotus purpuratus.

In this lab we will do some simple bootstrapping.

1. The file here has functions for computing bootstrapped Jukes-Cantor distances from an alignment file. Compute 100 bootstrapped trees using UPGMA from your alignment files from the previous lab. Write down the most common tree and include the bootstrap percentages on each bifurcation.
   To do this, you probably want to write a simple loop that stores the frequency of each tree. I recommend using a dictionary whose keys are the Newick strings from the upgma output, and whose values are the number of times that tree occurs.
2. Repeat the above exercise using the full mitochondrial genome for each species. The alignment files are here , here , and here. In case you need them, the original FASTA sequence files are here , here , and here. Be careful to correctly identify the species order when analysing your results - the .fa files may have a different order than the .aln files (sorry). Are your answers more reliable using the longer sequence?