CAFCA - Manual

CONTENTS

• Installation and Start-Up
• Overview of Menus
• Group Compatibility -- Primary Analysis
• Group Compatibility -- Secondary Analysis
• User-Tree Evaluation
• Component Compatibility
• References

I. Installation and Start-Up

• A short history of CAFCA
• License agreement
• Distribution Examples Installation
• Start-Up

II. Overview of menus

• OutputFile
  • Read ...
  • Save ...
  • Delete...
  • Undelete...
  • Trash...
  • Quit
• Run
  • Primary analysis...
  • Secondary Analysis...
  • Biogeographic Analysis...
  • User-tree Evaluation...
• Print
  • All Results...
  • Data matrix...
  • Partial sets...
  • Strict sets...
  • Diagram evaluation...
  • Diagrams...
  • States on root...
  • C.I for characters...
  • R.I. for characters...
  • Apomorphies & state changes...
• Utilities
  • Show free memory
  • Clear memory...
  • Clear screen
  • Clip data matrix...
  • Export data matrix data in NEXUS format...
  • data in PAUP-pc format...
  • data in SPECTRUM format...
  • data in MacClade 2.1 format...
  • data in NTSYS-pc format...
  • data in Hennig86 format...
• Ascii
  • Write file...
  • View file...
  • Delete file...
• Help
  • About CAFCA...
• Interrupt
  • Break
  • Pause output
  • Resume output

III. Group Compatibility - - Primary Analysis

• Introduction
• Example
  • Tutorial
  • Discussion of results
    • Header
      • Type of analysis.
      • Cladon option.
      • Cladogram selection.
      • Ancestors and outgroups.
      • Ordering of (multi-state) characters.
      • Number of cladograms.
    • Data Matrix
      • Types of characters, and the partitioning of columns.
        Polytypism.
      • Assumptions regarding zero's in the data matrix.
      • Full-zero columns
      • Missing values.
    • Clada
      1. Partial Monothetic Sets (PMS)
      2. Strict Monothetic Sets (SMS)
      3. PMS + all complementary codes
      4. PMS + All Additive Binary Codings (PMS + ABC)
      5. PMS + Three-Taxon-Statement Permutations (PMS + TTSP)
• Primary Analysis with Partial monothetic sets
  • Character states on root
  • Cladogram optimization.
  • Selection Criteria
    1. Homoplasous events
    2. Single origins
    3. Corrected Extra Length (CEL)
    4. Number of steps (Length)
    5. Redundancy Quotient (RQ)
    6. Rescaled Redundancy Quotient (RQc)
    7. Consistency Index (CI)
    8. Rescaled Consistency Index (RC)
    9. Average Unit Character Consistency (AUCC)
    10. Homoplasy distribution ratio (HDR)
    11. Compatible character state index (CCSI)
  • No-order lower limit
  • Un-informative characters
  • Diagrams, Apomorphies, and State Changes
• Primary Analysis with Strict monothetic sets
• Primary Analysis with All additive binary codings
• Primary Analysis with Three-taxon-statement permutations
• Analysis of data from taxa with a known phylogeny
• Comparison with character compatibility analysis
  • dePinna's data
  • Felsenstein's data
  • Meacham's data
  • Strauch's data
  • Anderson's data
• Comparison with Spectral Analysis
• Taxonomic efficiency
• Conclusion

IV. Group Compatibility - - Secondary Analysis

• Introduction
• Example
• Primary Analysis
  • Tutorial
  • Discussion of results
• Secondary Analysis
  • Tutorial
  • Discussion of results
• Using other options instead of secondary analysis
• Comparison with character compatibility analysis

V. User-Tree Evaluation

• Introduction
• Tutorial
• Discussion of results

VI. Component Compatibility

• Biogeographic Analysis
  • Area-cladogram
    • Introduction
    • Purpose
    • Assumptions
    • Basic data
    • Evaluation Example of an Analysis using Assumption Zero.
    • Tutorial
    • Discussion of results.
    • A critique of CCA
    • A comparison with BPA
    • Example of an Analysis using Assumption 1.
    • Missing areas and Redundancy
  • Generalized Area-cladogram
    • Introduction.
    • Example.
    • Tutorial
    • Discussion of results
    • Multi-state against binary area-data.
  • A comparison with BPA
  • A comparison with COMPONENT 2.0
• Co-Evolution
  • Introduction
  • Example
  • Recipe
  • Discussion of results

VII. References

Questions ?:  

© M. Zandee 1996-2003.