Practical: Bioinformatics 26/9/2012
We are reproducing distance analysis shown in this paper: Thomas,R.H. and Hunt,J.A."The molecular evolution of the alcohol dehydrogenase locus and the phylogeny of Hawaiian Drosophila, Mol. Biol. Evol. 8 (5), 687-702 (1991)

Get alcohol dehydrogenase gene, complete cds from the following 11 taxa:

D. melanogaster
D. pseudoobscura pseudoobscura
S. lebanonensis
S. albovittata
D. crassifemur
D. mulleri
D. affinidisjuncta
D. heteroneura
D. mimica
D. adiastola
D. nigra	


Create FASTA file for the unaligned sequences
Align FASTA sequences in MEGA
Calculate nucleotide base composition for all the taxa.
Calculate evolutionary distances (pairwise) using following substitution models, with standard error calculated using bootstrap method (1000 replicates):

1. JC69
2. K2P
3. Tamura-Nei
4. Maximum Composite Likelihood