PhyloGrapher was written very quickly and it was possible
because of a coincidence of several events in time and space such
as: code examples from "Tcl and the Tk Toolkit" by John Ousterhout,
"Practical Programming in Tcl and Tk" by Brent Welch, "Programming
Python" by Mark Lutz, and the
Open Source movement. I need to thank all people who shared their
ideas over the Internet. Also it would not be possible without the good
mood of my boss, Richard Michelmore. He had managed and set up excellent
conditions for extremely productive work. Some Tcl/Tk procedures were
re-used, originally implemented by Elena Kochetkova, an undergraduate student,
from our program
GenomePixelizer. I thank Heiko Schoof, MIPS, Institute for Bioinformatics,
Neuherberg, Germany for testing a beta version and for critical comments.
Of course, it would not be possible without NSF grant DBI-9975971
and a very nice California climate.
Graph Analysis Software
Pajek - Program for Large Network Analysis
Links to Graph Resources on the Web
Graphs and Graph Theory basic definitions at
MegaMath, Los Alamos National Laboratory
Graph Drawing Tutorial by Isabel Cruz and Roberto Tamassia
Graph Theory Glossary by Chris Caldwell at
Department of Mathematics and Statistics at
University of Tennessee, Martin
Graph and Digraph Glossary by Bill Cherowitzo
at the Mathematics Department, University of Colorado at Denver
Other useful links by David Eppstein,
Department of Information and Computer Science
at the University of California, Irvine.
Graph Theory in Bioinformatics
P Zhang, EA Schon, SG Fischer, E Cayanis, J Weiss, S Kistler, and PE Bourne. (1994)
An algorithm based on graph theory for the assembly of contigs
in physical mapping of DNA.
Comput. Appl. Biosci. 1994 10: 309-317.
A Krause and M Vingron. (1998)
A set-theoretic approach to database searching and clustering.
Bioinformatics 1998 14: 430-438.
X Guan and L Du. (1998)
Domain identification by clustering sequence alignments.
Bioinformatics 1998 14: 783-788.
HP Lenhof, B Morgenstern, and K Reinert. (1999)
An exact solution for the segment-to-segment multiple
sequence alignment problem.
Bioinformatics 1999 15: 203-210.
E Harley, A Bonner, and N Goodman. (1999)
Revealing hidden interval graph structure in STS-content data.
Bioinformatics 1999 15: 278-285.
Chantal Korostensky and Gaston H. Gonnet. (2000)
Using traveling salesman problem algorithms for evolutionary tree construction.
Bioinformatics 2000 16: 619-627.
Ying Xu, Dong Xu, and Harold N. Gabow. (2000)
Protein domain decomposition using a graph-theoretic approach.
Bioinformatics 2000 16: 1091-1104.
Frédéric Tores and Emmanuel Barillot. (2001)
The art of pedigree drawing: algorithmic aspects.
Bioinformatics 2001 17: 174-179.
Moritz Y. Becker and Isabel Rojas. (2001)
A graph layout algorithm for drawing metabolic pathways.
Bioinformatics 2001 17: 461-467.
Eric Harley, Anthony Bonner, and Nathan Goodman. (2001)
Uniform integration of genome mapping data using intersection graphs.
Bioinformatics 2001 17: 487-494.
Ken-ichiro Fukuda and Toshihisa Takagi. (2001)
Knowledge representation of signal transduction pathways.
Bioinformatics 2001 17: 829-837.
Anton J. Enright and Christos A. Ouzounis. (2001)
BioLayout-an automatic graph layout algorithm for similarity visualization.
Bioinformatics 2001 17: 853-854.
Eva Bolten, Alexander Schliep, Sebastian Schneckener,
Dietmar Schomburg, and Rainer Schrader. (2001)
Clustering protein sequences-structure prediction by transitive homology.
Bioinformatics 2001 17: 935-941.
Andrey Rzhetsky and Shawn M. Gomez. (2001)
Birth of scale-free molecular networks and the number of
distinct DNA and protein domains per genome.
Bioinformatics 2001 17: 988-996.
Frank Kose, Wolfram Weckwerth, Thomas Linke, and Oliver Fiehn.(2001)
Visualizing plant metabolomic correlation networks using
Bioinformatics 2001 17: 1198-1208.
Andreas Wagner. (2001)
How to reconstruct a large genetic network
from n gene perturbations in fewer than n2 easy steps.
Bioinformatics 2001 17: 1183-1197.
M. E. J. Newman. (2001)
From the Cover: The structure of scientific collaboration networks.
PNAS 98: 404-409.
Pavel A. Pevzner, Haixu Tang, and Michael S. Waterman. (2001)
An Eulerian path approach to DNA fragment assembly.
PNAS 98: 9748-9753.
Gabriel del Rio, Theodore F. Bartley, Heberto del-Rio, Rammohan Rao, KunLin Jin,
David A. Greenberg, Mark Eshoo and Dale E. Bredesen. (2001)
Mining DNA microarray data using a novel approach based on graph theory.
FEBS Letters, Volume 509, Issue 2, Pages 230-234.
Karasev VA, Stefanov VE. (2001)
Topological nature of the genetic code.
J Theor Biol. 2001 Apr 7;209(3):303-17.