TREECON for Windows user manual

A software package for the construction and drawing of evolutionary distance trees
Current version: 1.3b
Copyright © Yves Van de Peer Department of Biochemistry University of Antwerp (UIA), 1994, 1998
Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

**Table of Contents**
INTRODUCTION General information References and citation Acknowledgements Note
INSTALLATION OF TREECON Installation for Windows 95/NT Installation for Windows 3.x
GETTING STARTED Making a first tree using the default options
INPUT FILE FORMATS TREECON input file format PHYLIP input file format
DISTANCE ESTIMATION FOR NUCLEIC ACID SEQUENCES General introduction and Jukes and Cantor model Kimura - two parameter model Tajima & Nei Gamma distances Galtier & Gouy Transversion analysis No correction
DISTANCE ESTIMATION FOR AMINO ACID SEQUENCES Poisson correction Kimura Tajima & Nei Gamma distances
GENETIC DISTANCE ESTIMATION FOR PATTERN ANALYSIS Method 1 (Nei and Li, 1979) Method 2 (Link et al., 1995)
INSERTIONS AND DELETIONS
CHECK DISTANCE ESTIMATES
SUBSTITUTION RATE CALIBRATION General introduction How does substitution rate calibration works? A practical example on rate calibration
INFERRING TREE TOPOLOGIES Clustering and transformed distance Neighbor-joining
ROOTING UNROOTED TREES
BOOTSTRAP ANALYSIS Bootstrap analysis and rooting trees
DRAWING TREES General information Open trees in the draw program Drawing a newly constructed tree Loading previously constructed trees Saving and copying trees Saving trees in the TREECON format Saving trees in the HPGL format Saving trees as (DOS) text files Saving trees as Postscript files Copying trees to the clipboard Group Selection Group selection by different font Triangles Group shading Taxon designations Bootstrap values Rerooting a tree Scaling a tree Choosing a paper format Adding a distance scale Customizing a tree Drawing unrooted trees Options available in drawing unrooted trees Move unrooted tree Rotate unrooted tree Change angle of arc of the unrooted tree Drag branches Zoom unrooted tree Customize unrooted tree
OTHER TOOLS OF TREECON Construction of partial alignments Convert file formats Saving the TREECON input file as an alignment
FREQUENTLY ASKED QUESTIONS
KNOWN BUGS (BUT NOT YET SOLVED….)
REFERENCES
ABOUT THE AUTHOR

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