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3
Phylogenetic Analysis Workflows
This first example scenario is concerned with phylogenetic analyses. As they
are comparatively easy to understand (also for non-biologists) and there
is also a plethora of easy-to-use software tools available for the individual
analysis steps, phylogenetic analyses have become a frequently used, quasi-
standard application for illustrating bioinformatics workflow technology (cf.,
e.g., [256, 134, 155, 265, 165]). Furthermore, the annotation with seman-
tic meta-data is particularly advanced for this discipline [179], which is
advantageous for the application of the constraint-driven workflow design
methodology.
3.1 Background: Phylogenetics
The term
phylogenetics
refers to the analysis of evolutionary relationships
between different groups of organisms [279, p. 267]. While in former times
phylogenetic analyses were based on the examination of morphological and
physiological characters (the
phenotype
), modern molecular biology makes it
possible to take also genetic information (the
genotype
) into account. The
major carriers of genetic information are the
DNA
(deoxyribonucleic acid)
molecules, which are typically present in the form of a
double helix
.The
DNA double helix consists of two complementary nucleic acid strands that
are held together by hydrogen bonds between the bases
adenine
(A),
cytosine
(C),
guanine
(G), and
thymine
(T). These
base pairs
(bp) hold together the
two strands much like the rungs of a rope ladder. The
sequence
of the bases
in a nucleic acid strand constitutes the information that is carried by the
DNA molecule, that is,the individual
genes
that control specific features of
heredity. During cell division the DNA is replicated so that the offspring
obtains an identical copy of the genetic information. Another form of passing
genetic information to the next generation is DNA recombination, that is,
the assembly of genetic information from different sources into new sets of
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