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PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, free tree, and radial tree. With PhyloDraw users can manipulate the shape of a phylogenetic tree easily and interactively by using several control parameters. This program can export the final tree layout to BMP(bitmap image format) and Postscript.

   Input data
   Various tree type and interactive edit system
   Output form
   Sample
   Reference
 

Download

 PAPER

phylodraw.ps 

PROGRAM

PhyloDraw082.exe


Input data
PhyloDraw can import various output types of multialignment tools such as DIALIGN, Clustal-W, Phylip, Nexus, Mega, and pairwise distance matrix. Dialign and Clustal-W tools are available at http://www.gsf.de/biodv/dialign.html and http://www.fi.embnet.org/progs/clustalw. Pairwise distance matrix is a matrix of the evolutional distance between every pair of species, where the entry value of the pairwise distance matrix can be interactively manipulated by users. In constructing a phylogenetic tree from pairwise distance matrix, we provide two well-known clustering methods, UPGMA, Neighbor Joining, and Fitch and Magoliash.
 

Various tree type and interactive edit system
PhyloDraw support various types of drawings: free tree, radial tree, rooted tree, slanted cladogram, rectangle cladogram, and phylogram, and user can select the tree type interactively. All types of trees don't have edge crossing because they would prevent users from recognizing the phylogenetic information. Beyond PhyloDraw support interactive user editing function: resize the tree, and change the topology of the phylogenetic tree (rooted, unrooted, half-rooted), zoom in/out, etc.,
 

Output form
This system exports three types of output data (BMP, PostScript, and pairwise distace matrix) so that users can include them for word processors, graphics tools, and PostScript.
 

Sample
Input data (Phylip format )

 ((((((A00224:0.208083, A12705:0.208083) :0.145414, (A11522:0.132469, A18004:0.132469) :0.221028) :0.230361, ((A00660:0.110569, A09942:0.110569) :0.236883, A16386:0.347452) :0.236407) :0.173113, (A01530:0.594056, ((A05242:0.156023, A12565:0.156023) :0.316635, A16388:0.472658) :0.121398) :0.162916)

Tree drawing

 Free tree  

 Rooted tree  

 Radial tree  

 Rectangle cladogram  

 Slanted cladogram  

 Phylogram  

 

  Reference
[1] B.Morgenstern et al. DIALIGN : Finding local similarities by multiple sequence alignment. BIOINFORMATICS, 14(3):290-294, 1998.
[2] J.D.Thompson et al. Clustal W : Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22:4673-4680, 1994
[3] K.B.Nicholas et al. Genedoc: Analysis and visualization of genetic variation. EMBNEW.NEWS 4:14, 1997.
[4] G.Perriere and M.Gouy. WWW-Query : an online retrieval system for biological sequence banks. Biochimie, 78:364-369, 1996
[5] J.Felsenstein. Phylip : Phylogeny inference package. version 3.5. University of Washington, Seattle, WA, 1993.
[6] N.Saitou and M.Nei. The Neighbor-Joining method : a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4):406-425, Jul. 1987.
[7] P.H.A.Sneath and R.R.Sokal. UPGMA (Unweighted Pair-Group Method using Arithmetic averages). Jul. 1987.
[8] R.D.M.Page. Treeview : An application to display phylogenetic trees on personal computers. Computer Applications in the Biological Sciences, 12:357-358, 1996
[9] R.D.M.Page and M.A.Charleston. From gene to organismal phylogeny : Reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution, 7:231-240, 1997.
[10] W.H.E.Day. Computational complexity of inferring phylogenies from dissimilarity matrices. Bulletin of Mathematical Biology, 49:461-467, 1986.
 

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