PhyloGrapher Download:
Download current version April 03 2003.
BLAST parser
(This parser creates Matrix file for PhyloGrapher automatically using BLAST run results)
GenBank parser: GenBank_parser.py
MatrixMining page (How to set up a matrix for PhyloGrapher using ClustalW or FASTA output)
Download Tcl/Tk toolkit from tcl.activestate.com
What is new, April 03 2003:
Minor bug fixing (PhyloGrapher did not work properly if gene ID represented in numeric characters only,
e.g. GenBank identifier [GI]).
What is new, October 11 2002:
1. Project Configuration functionality. The user can choose any color scheme different
from default options. The nodes can be displayed as circles or ovals ("oval" option) as well as
as rectangles ("rect" option). Also size of nodes is flexible. User can choose custom URL prefix
and suffix to generate web pages.
2. Completely re-written canvas plot procedure is much faster than in previous version of PhyloGrapher.
3. PhyloGrapher now comes with BLAST parser to generate Matrix
automatically from BLAST output files.
What is new, March 15 2002:
1. Graph traversal (graph search) functionality. PhyloGrapher automatically detects and
highlights nodes belonging to distinct groups using DFS algorithm.
2. Font size for canvas labels and results of fasta search is changeable through
"Canvas Editor".
3. It is possible to save graphical results of fasta search as a postscript file.
What is new, February 07 2002:
Attempt to implement a modified version of Fruchterman Rheingold algorithm
to organize graph layout in automatic mode.
What is new, January 25 2002:
Graphical viewer results of FASTA or SSEARCH
(does work only if Bill Pearson's fasta package
is installed on your computer). Details of viewer usage see on the
PhyloGrapher Description web page.
What is new, December 01 2001:
1. display of edge weight
2. node degree counter
Download previous version October 11 2002.
Download previous version March 15 2002.
Download previous version December 01 2001.
Download first version September 12 2001.
Download Tcl/Tk toolkit from tcl.activestate.com
Quick Start
1. Extract compressed archive.
2. Go to the folder PhyloGrapher_April_03_2003.
3. on Linux run: PhyloGrapher_April_03_2003_Linux.tcl
on Windows run: PhyloGrapher_April_03_2003_Windows.tcl
4. Click on "Load Data into Memory". Wait several seconds,
after "beep" signal you should see the number 245
under the label "Number of Nodes".
5. Click "Run". Program should create the canvas with
nodes (genes) on it.
6. Click "Extras". On the new window click "Node Coords".
7. Then click "Restore" and watch the movie.
if fasta package is installed on your computer then:
8. From "Extras" menu click on "Smith-Waterman". New window should appear.
9. Point the mouse cursor on any node, press <Control-a>
10. Point the mouse cursor on another node, press <Control-s>
11. By clicking on "Show Alignment" PhyloGrapher should run FASTA or
SSEARCH of "node A" against of "node B"
and display results of search graphically
highlighting the critical parameters of an alignment.
graph traversal (graph search)
To test graph traversal (graph search) from extras choose
"Adjacency List". Click on "Build Adjacency List". Then
choose any node and click on "Highlight Adjacent Nodes"
or "Highlight All Nodes in Group".
manual drawing
To run PhyloGrapher in "Manual Drawing" mode (to draw custom graphs)
choose from "Project Configuration" window "Manual Drawing" option and
click "Run". The empty canvas should appear and using key "n" you can
create new node. To draw the edge from one node to another point mouse
over the first node and press "1" key, then point mouse over the second
node and press "2" key. New edge should appear.
