Phylogenetic analysis:
Sequence conservation across evolution

***There are some assumptions about evolution that underlie the science of molecular sequence analysis.
***DNA sequences of species (and sub-groups within species) change over time due to mutation.
***two species that have genes that are more similar in sequence are phlogenetically closer (and therefore separated by less evolutionary time) than are two species that have less sequence similarity.

***It should be possible to gather some sequence data from several different organisms, total up the differences, and determine their relationships.

***However, there are a number of hotly contested issues that interfere with this simplistic analysis.

***First, not all DNA sequences mutate at the same rate: protein coding regions mutate more slowly than non-coding regions.
***Second, some positions is protein coding DNA sequences are more free to mutate than others due to the redundancy of the genetic code.
***Beyond this lie the religious wars between adherents of parsimony vs. maximum likelihood methods of measuring distance.
***Given these problems, it is still possible to take a set of sequences and calculate phylogenetic distances and create a tree.

                           +----Thermosipho africanus
                           !               +---Fervidobacterium nodosum
                      +--8       +-----5
                      !    !        !       !    +--Fervidobacterium gondwanense
                      !    !        !       +--4
                      !    +-----6            +---Fervidobacterium islandicum
                      !             !
                      !             !       +---Petrotoga miotherma
                      !             +-----2
             +----10                     !    +---Geotoga subterrenea
             !        !                      +--1
             !        !                           +---Geotoga petrae
             !        !
             !        !         +---Thermotoga subterrenea
             !        !    +--7
   +------9        !    !    +--Thermotoga elfii
   !         !        +-12
   !         !             !    +---Thermotoga hypogea
   !         !             +-11
   !         !                  +----Thermotoga thermarum
   !         !
   !         +----Thermotoga maritima
   3------Aquifex pyrophilus

***The problem faced by the researcher is to choose which of nearly 100 different software tools to use.

Computers in Molecular Microbiology
Bharat Patel, Biomolecular & Biomedical Sciences, Griffith University, Australia
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