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Bionomics International produces several software products which are available to the educational and scientific community. These products are primarily distributed as shareware. Certain of these products are freely available to individuals who are associated with several Bionomics International projects,  e.g. Canadian Blind Study.

Database Management

     MICRO-IS functions as a computer-based laboratory notebook for culture collection or field data, both phenotypic and genomic, and as the basis for either printed or electronic collection catalogue production. The resulting database is usable in such applications as identification, taxonomy, ecology, epidemiology, biosafety, bioremediation, food safety and quality, screening programs, genetic engineering studies, product development, Current Good Manufacturing Practices, and education

Numerical Analysis

       EDITMAT is an interactive program which edits matrices of binary information (phenetic data) and provides basic information about the data. EDITMAT provides the following functions, all of which are optional and usable in any combination:

  1. Tabulates the number of positive, negative, and missing items by feature and/or Operational Taxonomic Unit (OTU).
  2. Calculates and prints tables of frequency of positive, negative, and missing items by feature and/or OTU .
  3. Delete user specified features and/or OTUs.
  4. Deletes features and/or OTUs based on user-set thresholds. That is, deletes all features and/or OTUs that have little or no separating significance.
  5. Lists a summary of deletions of OTUs and features.
  6. Gives rank of OTU and/or feature by positive frequency.
  7. Rearranges data in order of positive OTU frequency.
  8. Collates data for input into programs requiring a collated format.
  9. Allows for multiple passes to facilitate refinement of the data.

     REORDER rearranges a list of coded items into any order using a separate list of alphabetic sort codes. For example, REORDER is used to arrange strain data into the taxonomic order found in a similarity triangle or dendrogram from cluster analysis.  REORDER can also be used to sort, coded,  multiline information where the number of lines per item may be variable.

     FREAK is a program for tabulating the occurrence of binary (yes/no) character states (i.e. features) according to their frequency of occurrence within a set of strains or any subgroup of this set.  Output from Freak contains the following information.

  1. A list of the code designations of Operational Taxonomic Units (OTU) in each group.
  2. A table giving the positive, negative and missing counts of each character for all (overall) OTUs and each group of OTUs.
  3. A table of the percentage of OTUs, overall and in each group, that have positive characteristics.
  4. A table giving the level of uniqueness of a character for each group and a table giving the group partitioning index.
  5. A table of the hypothetical modal organism (HMO) for each group.
  6. A list of the similarity of each OTU to the overall HMO and the group HMO using either the simple matching coefficient (Sm) or the Jaccard coefficient (Sj), OTUs are listed in unsorted and sorted order.
  7. The taxon radius and Vigor is calculated for each group.
  8. Generate similarity or distance matrices using Gower Coefficients.
  9. A probabilistic matrix can be created from the data and may be output in either MICRO-IS format or a general format used by other programs.

   VOTE is taxonomic analysis program which provides three functions:

  1. It counts the frequency of occurrence of each pattern of features regardless of the Operational Taxonomic Unit (OTU) ID.
  2. It generates a hypothetical modal OTU for any number of repeated or replicate binary features with the same OTU ID.
  3. It can be used to eliminate duplicate OTU IDs.

Last Modified: January 08, 2011
Bionomics International
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Wheaton, Maryland 20902