Constructing Phenetic and Phylogenetic Relationship Using Clad'97

Abstract

Relationship construction has a very important position in classification process for arranging taxonomy of organism.
In the world of taxonomy, there are two the most familiar relationship diagram, cladogram and phenogram. In every
construction activity, a researcher is always facing character state data from taxa that becomes components of the
diagram. Calculation that is used for construction is often incorporate iterative or repetitive process that needs time
and precision. The existence of calculating tools that produces both text and graphical output are hopefully decrease
time and error during construction. Basic algorithm that is used in calculation is for phylogenetic construction by
Kluge and Farris in 1969,for phenetic construction using cluster analysis with slight modification. Basic common
algorithm used in the software is by calculating two dimensional arrays of taxa x characters matrix and creating
distance or similarity matrix. In more detail the program creates one dimensional array of taxonomical object and
each object has some other one dimensional array containing data commonly exist in a taxonomic unit. The
relationship between one object and theother are regulated by an object that created by class representing taxonomic
tree. Cladogram is constructed by calculating nearest distance between each taxon (OTU) and creating one HTU in
every bifurcation. Phenogram is constructed agglomeratively by searching highest similarity between taxon then
grouped into new taxon. Program calculates numerical data after we do character scoring. Final result for each user
may be different; this may be due to decision by user during construction process. This paper hopefully attracts
people from systematic computation to develop further into open source software and multi-platform feature.