DisplayFam is a browser for the analysis of multiple alignments of large numbers of protein sequences. DisplayFam users must cite: F. Corpet, J. Gouzy and D. Kahn (1999), "Browsing protein families via the 'Rich Family Description' data structure.", Bioinformatics, 15:12, 1020-1027. For more information e-mail to proquest@toulouse.inra.fr Table of contents: Presentation Installation List of files Copyrights Presentation: DisplayFam.pl is a Perl script that runs with CGI input. It must be installed in a cgi-bin directory (see your web server documentation). DisplayFam.pl first part must be edited with your personal configuration : see DisplayFam.pl part 1, comment lines. It is safer to keep a version of the original file before editing it! DisplayFam.pl looks for an rfd file using id_fam parameter value and sends back a dynamically built html page. This page displays the family using the other parameters. It includes a form that call DisplayFam again to display the family with new parameters (see DisplayFam.pl part 4 or Bioinformatics paper for details). The process that finds the rfd file is user-defined ($FETCHFAM). An example is provided that looks for a file called "id_fam.in" in the temporary directory or translates a msf alignment to an rfd file if id_fam equals 'new' (see msf2rfd.html as a form example and the original DisplayFam.pl): cgi-bin/DisplayFam.pl?id_fam=new&msf=file_name.msf or cgi-bin/DisplayFam.pl?id_fam=new&alignment=msf_data Installation : To install DisplayFam you need : - a cgi-bin directory with DisplayFam.pl and cgi-lib2.pl - a working directory ($PROG) with the softwares and their data files: protdist, bionj, TriangleTree, reroot, consens, subtree, drawtree species. This directory must give r, w and x rights to the world. - an image directory (which url is $HTTPIMAGE) with the gif files plus, redball, triangle, (yellow, blue, red, green, black)square, alignment, tree - a temporary directory ($DOMDIR, which url is $HTTPDATA) with r and w rights to the world. List of files included in this package: Example of html form msf2rfd.html Perl scripts DisplayFam.pl cgi-lib2.pl images plus.gif redball.gif triangle.gif yellowsquare.gif bluesquare.gif redsquare.gif greensquare.gif blacksquare.gif alignment.gif tree.gif programs and their data files protdist bionj TriangleTree reroot consens subtree drawtree species Copyrights: DisplayFam users must cite: F. Corpet, J. Gouzy and D. Kahn (1999), 'Browsing protein families via the "Rich Family Description" data structure.', Bioinformatics, 15:12, 1020-1027. cgi-lib2.pl: # Perl Routines to Manipulate CGI input # cgi-lib@pobox.com # $Id: cgi-lib.pl,v 2.18 1999/02/23 08:16:43 brenner Exp $ # # Copyright (c) 1993-1999 Steven E. Brenner # Unpublished work. # Permission granted to use and modify this library so long as the # copyright above is maintained, modifications are documented, and # credit is given for any use of the library. # For more information, see: # http://cgi-lib.stanford.edu/cgi-lib/ protdist is a mix of Phylip protdist and Guénoche missdist protdist: version 3.5c PROTDIST -- Program to compute distance matrix from protein sequences (c) Copyright 1993 by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. missdist: MissDist function (15 February 1999). A. Guenoche, L. Duret + modif 17 March 1999 bionj: /*;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ; ; ; BIONJ program ; ; ; ; Olivier Gascuel ; ; ; ; GERAD - Montreal- Canada ; ; olivierg@crt.umontreal.ca ; ; ; ; LIRMM - Montpellier- France ; ; gascuel@lirmm.fr ; ; ; ; UNIX version, written in C ; ; by Hoa Sien Cuong (Univ. Montreal) ; ; ; \*;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*/ TriangleTree: version 1 - 15/01/98 TriangleTree function Alain Guenoche (1), Laurent Duret (2), Bruno Leclerc (3) The triangles method to build phylogenetic trees from incomplete distance matrices. (1) Laboratoire d'Informatique de Marseille, 163 Av de Luminy, 13009 Marseille, France guenoche@lim.univ-mrs.fr (2) Laboratoire BGBP - UMR CNRS 5558 Universite Claude Bernard - Lyon 1 43 Bd du 11 Novembre 1918 69622 Villeurbanne Cedex, France duret@biomserv.univ-lyon1.fr (3) Centre d'Analyse et de Mathematique Sociales Ecole des Hautes Etudes en Sciences Sociales 54 Bd Raspail 75270 Paris cedex 06, France leclerc@ehess.fr drawtree is a mix of Phylip programs and personal functions that use a gif library drawtree: version 3.5c DRAWTREE (c) Copyright 1990-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. gif library: gd 1.2 is copyright 1994, 1995, Quest Protein Database Center, Cold Spring Harbor Labs. Permission granted to copy and distribute this work provided that this notice remains intact. Credit for the library must be given to the Quest Protein Database Center, Cold Spring Harbor Labs, in all derived works. This does not affect your ownership of the derived work itself, and the intent is to assure proper credit for Quest, not to interfere with your use of gd. If you have questions, ask. ("Derived works" includes all programs that utilize the library. Credit must be given in user-visible documentation.) gd 1.2 was written by Thomas Boutell and is currently distributed by boutell.com, Inc. If you wish to release modifications to gd, please clear them first by sending email to boutell@boutell.com; if this is not done, any modified version of the gd library must be clearly labeled as such. The Quest Protein Database Center is funded under Grant P41-RR02188 by the National Institutes of Health. Written by Thomas Boutell, 2/94 - 8/95. The GIF compression code is based on that found in the pbmplus utilities, which in turn is based on GIFENCOD by David Rowley. See the notice below: /* ** Based on GIFENCOD by David Rowley .A ** Lempel-Zim compression based on "compress". ** ** Modified by Marcel Wijkstra ** ** Copyright (C) 1989 by Jef Poskanzer. ** ** Permission to use, copy, modify, and distribute this software and its ** documentation for any purpose and without fee is hereby granted, provided ** that the above copyright notice appear in all copies and that both that ** copyright notice and this permission notice appear in supporting ** documentation. This software is provided "as is" without express or ** implied warranty. ** ** The Graphics Interchange Format(c) is the Copyright property of ** CompuServe Incorporated. GIF(sm) is a Service Mark property of ** CompuServe Incorporated. */ The GIF decompression is based on that found in the pbmplus utilities, which in turn is based on GIFDECOD by David Koblas. See the notice below: /* +-------------------------------------------------------------------+ */ /* | Copyright 1990, 1991, 1993, David Koblas. (koblas@netcom.com) | */ /* | Permission to use, copy, modify, and distribute this software | */ /* | and its documentation for any purpose and without fee is hereby | */ /* | granted, provided that the above copyright notice appear in all | */ /* | copies and that both that copyright notice and this permission | */ /* | notice appear in supporting documentation. This software is | */ /* | provided "as is" without express or implied warranty. | */ /* +-------------------------------------------------------------------+ */