Python Programming for Biology: Bioinformatics and Beyond

Phylogenetic trees

Moving on from the more basic ways of considering substitutions and alignments, the next

examples  relate  to  the  generation  of  phylogenetic  trees.  These  are  branching  structures

which  in  general  aim,  however  falteringly,  to  represent  the  order  in  which  different  taxa

(the sequences, species, strains etc. being compared) diverged from one another during the

process of evolution. The aim is to give the order of the divergence and the evolutionary

distance  between  the  branch  points  and  observed  sequence  data.  Naturally,  the  more

information  is  available  the  better  the  chances  are  of  a  computer-generated  tree  having

accurate  evolutionary  distances  and  the  real,  historical  divergence  order.  However,  it

should  be  noted  that  you  can  always  generate  a  tree,  however  bad  or  uninformative  the

data, so caution is always advised in estimating the true, underlying relationship.