Journal of Tropical Life Science, Vol 2, No 1 (2012)

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Constructing Phenetic and Phylogenetic Relationship Using Clad'97

Brian Rahardi, Estri Laras Arumningtyas, Wayan Firdaus Mahmudi

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.

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