Phylogenetics Homework 3

Use the protein and DNA sequence alignments of the 6-phosphogluconate dehydrogenase, decarboxylating (gnd) protein and DNA sequences for the following species:

Encephalitozoon cuniculi (Fungus)
Dictyostelium discoideum (Slime mold)
Synechococcus elongatus (Cyanobacteria)
Cronobacter dublinensis (Proteobacteria)
Candidatus Solibacter usitatus (Acidobacteria)
Leptotrichia goodfellowii (Fusobacteria)
Borrelia garinii (Spirochaetes)
Phycisphaera mikurensis (Planctomycetes)
Mycobacterium tuberculosis (Actinobacteria)
Anaerolinea thermophila (Chloroflexi)
Chlamydia trachomatis (Chlamydiae)
Lactococcus lactis (Firmicutes)

from the your last homework assignment to create the following pairwise distance matrices for these species. Tell which software package you used to compute these distances.

  1. Distances from the protein sequence alignment using
    1. PAM250
    2. BLOSUM62
    3. Another method of your choice
  2. Distances from the DNA sequence alignment:
    1. Jukes-Cantor distances
    2. Tamura and Nei (1993) distances
    3. logdet distances
    4. Another method of your choice
Packages seqinr, bios2mds, and ape in R can be used for these computations. Phylogeny software such as Phylip and MEGA and PAUP can be used to find certain pairwise distance matrices as well.