title: DIPLOMO: the tool for a new type of evolutionary analysis.
abstract: A package of computer programs called DIPLOMO (DIstance PLOt MOnitor) has been developed for making pairwise comparisons of different estimates of the distances between a set of taxa by plotting them against each other in a simple scatter plot. Taxa with similar relative distance characteristics are thereby grouped graphically. Groupings of different taxa may be directly identified, and the distance characteristics of chosen groups visualised and compared using devices to give them different colours or symbols. The program is particularly useful for detecting and analysing subtle trends in gene sequence evolution. This is done by comparing different components of change, for example synonymous versus non-synonymous nucleotide changes, transversions versus transitions and changes in different genes of the same set of taxa, etc. The program has a wide range of other uses, for example comparing different methods of sequence analysis, assessing which components of genetic change correlate best with phenotypic change or with geographical separation. This paper describes the DIPLOMO package, and illustrates typical DIPLOMO analyses using lentivirus gene sequence data.
authors.affiliation: Research School of Biological Science, Australian National University, Camberra, Australia. weiller@rsbscentral.anu.edu.au
authors.forename: G F
authors.initials: GF
authors.lastname: Weiller
authors.forename: A
authors.initials: A
authors.lastname: Gibbs
mesh_terms: D005075:Biological Evolution; D005069:Evaluation Studies as Topic; D015752:Genes, env; D005821:Genetic Techniques; D015497:HIV-1 / Q000235:genetics; D015498:HIV-2 / Q000235:genetics; D015302:Simian Immunodeficiency Virus / Q000235:genetics; D012984:Software; D013045:Species Specificity