1. Sequence alignment

2. aligned sequences substitution model

3. Jukes Cantor, one parameter,  AG TC      

4. AG TC       Kimura 2 parameter model,  ts: transitions tv: transversions  

5. Other models Tajima-Nei Tamura 3 parameter Tamura-Nei Pevsner 2009

6. Choosing the substitution model p-distaceEqual Jukes-Cantor 1 type of substitutions, ts=tv Kimura 2 parameter 2 substitution types, ts≠tv Unequal Tajima-Nei 1 type of substitutions, ts=tv Tamura 3- parameter 2 substitution types, ts≠tv Tamura-Nei 3 types of substitutions, CT≠AG≠tv Nucleotide frequencies ts: transitions tv: transversions