academic/treeview: Added (Program to display phylogenetic trees)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

9 files changed, 1966 insertions, 0 deletions

diff --git a/academic/treeview/README b/academic/treeview/README
new file mode 100644
index 0000000000000..86281f2a43c70
--- /dev/null
+++ b/academic/treeview/README
@@ -0,0 +1,21 @@
+TreeView is a simple program for displaying phylogenies. Some of its
+features include:
+
+- reads many different tree file formats (including NEXUS, PHYLIP, 
+  Hennig86, NONA, MEGA, and ClustalW/X)
+- supports standard the TrueType and Postscript fonts
+- supports native graphics file format for copying pictures into 
+  other applications, and for saving graphics files
+- print preview
+- can print multiple trees per page and/or one tree over more than 
+  one page
+- has drag-and-drop facility for easy opening of files
+- Web-based online help
+- tree editor
+
+For details and citation:
+Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic 
+trees on personal computers. Computer Applications in the Biosciences 
+12: 357-358. 
+
+This requires wxGTK or wxPython, available at SlackBuilds.org.
diff --git a/academic/treeview/References b/academic/treeview/References
new file mode 100644
index 0000000000000..c5c8df7b7fdfb
--- /dev/null
+++ b/academic/treeview/References
@@ -0,0 +1 @@
+Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358. 
\ No newline at end of file
diff --git a/academic/treeview/doinst.sh b/academic/treeview/doinst.sh
new file mode 100644
index 0000000000000..5fb28930db0b9
--- /dev/null
+++ b/academic/treeview/doinst.sh
@@ -0,0 +1,3 @@
+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
diff --git a/academic/treeview/slack-desc b/academic/treeview/slack-desc
new file mode 100644
index 0000000000000..1df5c90d4efbc
--- /dev/null
+++ b/academic/treeview/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.  Line
+# up the first '|' above the ':' following the base package name, and the '|'
+# on the right side marks the last column you can put a character in.  You must
+# make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':'.
+
+        |-----handy-ruler------------------------------------------------------|
+treeview: treeview (Program to display phylogenetic trees)
+treeview:
+treeview: TreeView provides a simple way to view the contents of a NEXUS,
+treeview: PHYLIP, Hennig86, Clustal, or other format tree file.
+treeview:
+treeview:
+treeview:
+treeview:
+treeview:
+treeview: References: /usr/doc/treeview-$VERSION/References
+treeview: Home: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/
diff --git a/academic/treeview/treeview.SlackBuild b/academic/treeview/treeview.SlackBuild
new file mode 100644
index 0000000000000..2823c5276161f
--- /dev/null
+++ b/academic/treeview/treeview.SlackBuild
@@ -0,0 +1,109 @@
+#!/bin/sh
+
+# Slackware build script for treeview
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
+# hereby submitted to the public domain
+
+# Based on the treeview PKGBUILD from Archlinux AUR 
+# (http://aur.archlinux.org/packages.php?ID=19489). 
+# PKGBUILD submitter is abhidg and PKGBUILD maintainer 
+# is Stunts. Thank you!
+
+# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING 
+# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ 
+# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+
+PRGNAM=treeview
+VERSION=${VERSION:-0.5.1}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+SRCNAM=tv
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) export ARCH=i486 ;;
+    arm*) export ARCH=arm ;;
+       *) export ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i486" ]; then
+  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+# The patch is from Archlinux AUR, as mentioned above. 
+# For AUR it has been taken from Debian. Thank you both!
+patch -p1 < $CWD/treeviewx_0.5.1-7.diff
+for i in ./debian/patches/*.diff; do
+patch -p1 < $i
+done
+
+# Disable SVG support. If you want it, you should build 
+# wxGTK or wxPython including svg from contrib/src/svg
+# Then, of course comment the next line.
+sed "s:USE_SVG=1:USE_SVG=0:" -i configure
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --build=$ARCH-slackware-linux
+
+make
+make install DESTDIR=$PKG
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/tv.desktop $PKG/usr/share/applications
+cp $CWD/tv.png $PKG/usr/share/pixmaps
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  COPYING INSTALL \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/treeview/treeview.info b/academic/treeview/treeview.info
new file mode 100644
index 0000000000000..8fba131fb2511
--- /dev/null
+++ b/academic/treeview/treeview.info
@@ -0,0 +1,10 @@
+PRGNAM="treeview"
+VERSION="0.5.1"
+HOMEPAGE="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html"
+DOWNLOAD="http://darwin.zoology.gla.ac.uk/%7Erpage/treeviewx/download/0.5/tv-0.5.1.tar.gz"
+MD5SUM="07e1ed8873c5f19ded7294668233bae1"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/treeview/treeviewx_0.5.1-7.diff b/academic/treeview/treeviewx_0.5.1-7.diff
new file mode 100644
index 0000000000000..dc9c12c204b4c
--- /dev/null
+++ b/academic/treeview/treeviewx_0.5.1-7.diff
@@ -0,0 +1,1796 @@
+--- treeviewx-0.5.1.orig/debian/watch
++++ treeviewx-0.5.1/debian/watch
+@@ -0,0 +1,2 @@
++version=3
++http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html download\/\d\.\d\/tv-(\d+)\.(\d+)\.(\d+)\.tar\.gz
+--- treeviewx-0.5.1.orig/debian/treeviewx.sharedmimeinfo
++++ treeviewx-0.5.1/debian/treeviewx.sharedmimeinfo
+@@ -0,0 +1,13 @@
++<?xml version="1.0"?>
++<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
++  <mime-type type="text/x-clustalw-tree">
++    <comment>Phylogenetic tree in Clustal W format</comment>
++    <comment xml:lang="fr">Arbre phylogénétique au format Clustal W</comment>
++    <comment xml:lang="it">Albero filogenetico in formato Clustal W</comment>
++    <magic priority="50">
++      <match type="string" offset="0" value="(\n"/>
++    </magic>
++    <glob pattern="*.phb"/>
++    <glob pattern="*.ph"/>
++  </mime-type>
++</mime-info>
+--- treeviewx-0.5.1.orig/debian/menu
++++ treeviewx-0.5.1/debian/menu
+@@ -0,0 +1,8 @@
++?package(treeviewx):\
++	needs="X11"\
++	section="Applications/Science/Biology"\
++	title="TreeView X"\
++	command="/usr/bin/tv"\
++	icon="/usr/share/pixmaps/treeviewx.xpm" \
++	hints="Phylogenetic tree drawing program"\
++	longtitle="TreeView X: a phylogenetic tree viewer which can do SVG export"
+--- treeviewx-0.5.1.orig/debian/rules
++++ treeviewx-0.5.1/debian/rules
+@@ -0,0 +1,8 @@
++#!/usr/bin/make -f
++
++include /usr/share/cdbs/1/class/autotools.mk
++include /usr/share/cdbs/1/rules/patchsys-quilt.mk
++include /usr/share/cdbs/1/rules/debhelper.mk
++
++install/treeviewx::
++	install -m 644 bitmaps/treeview.xpm $(CURDIR)/debian/treeviewx/usr/share/pixmaps/treeviewx.xpm
+--- treeviewx-0.5.1.orig/debian/upstream-metadata.yaml
++++ treeviewx-0.5.1/debian/upstream-metadata.yaml
+@@ -0,0 +1,14 @@
++Contact: Roderic D. M. Page <r.page@bio.gla.ac.uk>
++DOI: 10.1093/bioinformatics/12.4.357
++Homepage: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ 
++Name: Treeview X
++PMID: 8902363 
++Reference-Author: Page, Roderic D. M.
++Reference-Journal: Comput. Appl. Biosci.
++Reference-Number: 4
++Reference-Page: 357-8
++Reference-Title: TreeView: an application to display phylogenetic trees on personal computers
++Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357
++Reference-Volume: 12
++Reference-Year: 1996
++Watch: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html download\/\d\.\d\/tv-(\d+)\.(\d+)\.(\d+)\.tar\.gz
+--- treeviewx-0.5.1.orig/debian/control
++++ treeviewx-0.5.1/debian/control
+@@ -0,0 +1,22 @@
++Source: treeviewx
++Section: science
++Priority: optional
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++DM-Upload-Allowed: yes
++Uploaders: Charles Plessy <plessy@debian.org>,
++ Andreas Tille <tille@debian.org>
++Build-Depends: debhelper (>= 7.1), cdbs, autotools-dev, quilt, libwxgtk2.8-dev
++Standards-Version: 3.8.4
++Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/treeviewx/trunk/?rev=0&sc=0
++Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/treeviewx/trunk/
++Homepage: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/
++
++Package: treeviewx
++Architecture: any
++Depends: ${shlibs:Depends}, ${misc:Depends}
++Description: Displays and prints phylogenetic trees
++ TreeView X is an open source and multi-platform program to display
++ phylogenetic trees. It can read and display NEXUS and Newick format tree files
++ (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It
++ allows to order the branches of the trees, and to export the trees in SVG
++ format.
+--- treeviewx-0.5.1.orig/debian/copyright
++++ treeviewx-0.5.1/debian/copyright
+@@ -0,0 +1,61 @@
++Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5’.
++
++Name   :  TreeView X
++Author :  Roderic D. M. Page <r.page@bio.gla.ac.uk>
++Source :  http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz
++
++License: GPL-2+
++   
++   TreeView X is free software; you can redistribute it and/or modify
++   it under the terms of the GNU General Public License as published by
++   the Free Software Foundation; either version 2 of the License, or
++   (at your option) any later version.
++   
++   TreeView X is distributed in the hope that it will be useful,
++   but WITHOUT ANY WARRANTY; without even the implied warranty of
++   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
++   GNU General Public License for more details.
++   
++   You should have received a copy of the GNU General Public License
++   along with this package; if not, write to the Free Software
++   Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++
++TreeView X has been released by its author under the GNU GPL (see COPYING), but
++most of its files use a header which places them under the GNU Library GPL
++(LGPL). The author of TreeView X confirmed to the maintainer of this package
++that his intention is to have TreeView X released under the GPL. Therefore, as
++permitted the clause 3 of the LGPL, the licence of these files is changed to
++the GPL through the patch in the following file:
++debian/patches/60_LGPLtoGPL.dpatch
++
++Some files which are part of TreeView X - namely ntree.h, ntree.cpp and
++lcaquery.cpp - have no copyright notice. The author of TreeView X confirmed to
++the maintainer of this package that he is the copyright holder for them.
++Therefore, they are distributed under the terms of the COPYING file, which is
++the GNU GPL.
++
++On Debian systems, the complete text of the GNU Library General Public
++License can be found in ‘/usr/share/common-licenses/LGPL-2’ and the
++complete text of the GNU General Public License version 2 can be found
++in ‘/usr/share/common-licenses/GPL-2’.
++
++Files: ncl-2.0/*
++Copyright: © 1999 Paul O. Lewis
++License: GPL-2+
++Comment: TreeView X is statically linked to the Nexus Class Library.
++
++Files: TreeLib/*
++Copyright: © 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++License: GPL-2+
++Comment: The files under the TreeLib directory are part of TreeView X,
++ as they have never been released as an independent library.
++
++Files: debian/tv.1.xml debian/tv.1
++Copyright: © 2006-2008 Charles Plessy <charles-debian-nospam@plessy.org>
++License: Same as TreeView X
++
++Files: debian/*
++Copyright: © 2006–2010 Charles Plessy <plessy@debian.org>
++           © 2007 David Paleino <d.paleino@gmail.com>
++License: PD
++ Please treat the packaging work as if it were in the public domain.
+--- treeviewx-0.5.1.orig/debian/treeviewx.mime
++++ treeviewx-0.5.1/debian/treeviewx.mime
+@@ -0,0 +1 @@
++text/x-clustalw-tree; /usr/bin/tv '%s'; description=ClustalW Phylogenetic Tree
+--- treeviewx-0.5.1.orig/debian/manpages
++++ treeviewx-0.5.1/debian/manpages
+@@ -0,0 +1 @@
++debian/tv.1
+--- treeviewx-0.5.1.orig/debian/README.source
++++ treeviewx-0.5.1/debian/README.source
+@@ -0,0 +1,4 @@
++This packages uses the quilt patch system. Please read
++/usr/share/doc/quilt/README.source for more information.
++
++ -- Andreas Tille <tille@debian.org>  Mon, 31 Aug 2009 14:50:19 +0200
+--- treeviewx-0.5.1.orig/debian/dirs
++++ treeviewx-0.5.1/debian/dirs
+@@ -0,0 +1,2 @@
++/usr/share/applications
++/usr/share/pixmaps
+--- treeviewx-0.5.1.orig/debian/treeviewx.desktop
++++ treeviewx-0.5.1/debian/treeviewx.desktop
+@@ -0,0 +1,19 @@
++[Desktop Entry]
++Version=1.0
++Terminal=false
++Icon=treeviewx
++Exec=tv %f
++Name=TreeView X
++GenericName=Tree Plotter
++GenericName[en]=Tree Plotter
++GenericName[fr]=Traceur d'arbres
++GenericName[pt_BR]=Plotador de árvores
++GenericName[it]=Plotter di Alberi
++Comment=Displays, modifies, prints and exports in SVG format phylogenetic trees
++Comment[en]=Displays, modifies, prints and exports in SVG format phylogenetic trees
++Comment[fr]=Affiche, modifie, imprime et exporte au format SVG des arbres phyolgénétiques
++Comment[pt_BR]=Exibe, modifica e exporta em formato SVG árvores filogenéticas
++Comment[it]=Mostra, modifica, stampa ed esporta in formato SVG alberi filogenetici
++Type=Application
++Categories=Biology;Science;Education;
++MimeType=text/x-clustalw-tree;
+--- treeviewx-0.5.1.orig/debian/tv.1.xml
++++ treeviewx-0.5.1/debian/tv.1.xml
+@@ -0,0 +1,109 @@
++<?xml version='1.0' encoding='UTF-8'?>
++<?xml-stylesheet type="text/xsl"
++	href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
++<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
++	"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
++
++  <!ENTITY dhfirstname "<firstname>Charles</firstname>">
++  <!ENTITY dhsurname   "<surname>Plessy</surname>">
++  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
++  <!ENTITY dhemail     "<email>charles-debian-nospam@plessy.org</email>">
++  <!ENTITY dhusername  "Charles Plessy">
++  <!ENTITY dhucpackage "<refentrytitle>TREEVIEW X</refentrytitle>">
++  <!ENTITY dhpackage   "tv">
++  <!ENTITY debian      "<productname>Debian</productname>">
++  <!ENTITY gnu         "<acronym>GNU</acronym>">
++  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
++]>
++
++<refentry>
++  <refentryinfo>
++    <address>
++      &dhemail;
++    </address>
++<!--    <author>
++      &dhfirstname;
++      &dhsurname; 
++    </author>  -->
++    <copyright>
++      <year>2006</year>
++      <year>2008</year>
++      <holder>&dhusername;</holder>
++    </copyright>
++  </refentryinfo>
++  <refmeta>
++    &dhucpackage;
++
++    &dhsection;
++  </refmeta>
++  <refnamediv>
++    <refname>&dhpackage;</refname>
++
++    <refpurpose>displays and prints phylogenetic trees</refpurpose>
++  </refnamediv>
++  <refsynopsisdiv>
++    <cmdsynopsis>
++      <command>tv</command> <arg choice="opt"><replaceable>filename</replaceable></arg>
++    </cmdsynopsis>
++  </refsynopsisdiv>
++  <refsect1>
++    <title>DESCRIPTION</title>
++
++
++    <para><command>tv</command> is the program that starts the
++    TreeView X GUI.</para>
++    
++    
++     <para>TreeView X is an open source and multi-platform program to
++     display phylogenetic trees. It can read and display NEXUS and
++     Newick format tree files (such as those output by PAUP*,
++     ClustalX, TREE-PUZZLE, and other programs). It allows to order
++     the branches of the trees, and to export the trees in SVG
++     format.</para>
++
++     <para>If started from the command line with
++     <filename>filename</filename> as an argument, TreeView X
++     will open the tree stored in <filename>filename</filename>.</para>
++
++	     
++  </refsect1>
++
++  <refsect1>
++    <title>SEE ALSO</title>
++
++    <para>
++        At present there is is no documentation for TreeView X. In the
++    meantime please see the online documentation for TreeView
++    (remember that TreeView X has only a subset of the features of
++    TreeView). http://taxonomy.zoology.gla.ac.uk/rod/treeview/treeview_manual.html
++      </para>
++  </refsect1>
++
++  <refsect1>
++    <title>REFERENCE</title>
++    <para>Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.</para>
++  </refsect1>
++      
++  <refsect1>
++    <title>AUTHOR</title>
++
++     <para><application>TreeView X</application> was written by Rod
++     Page (r.page@bio.gla.ac.uk) URL:
++     http://darwin.zoology.gla.ac.uk/~rpage/treeviewx.</para>
++
++    <para>This manual page was written by &dhusername; (&dhemail;) for
++      the &debian; system (but may be used by others).</para>
++      
++      <!-- You can  copy, distribute and/or modify this document under the same terms as TreeView X itself. -->
++      
++    <para>
++      Permission is granted to copy, distribute and/or modify TreeView X and this document under the terms of the &gnu; General Public License, Version 2 or any later version published by the Free Software Foundation.
++    </para>
++	
++    <para>
++      On Debian systems, the complete text of the GNU General Public
++      License can be found in /usr/share/common-licenses/GPL.
++    </para>
++
++  </refsect1>
++</refentry>
+--- treeviewx-0.5.1.orig/debian/tree.phb
++++ treeviewx-0.5.1/debian/tree.phb
+@@ -0,0 +1,55 @@
++(
++(
++(
++(
++(
++(
++(
++(
++(
++gi|6981382|ref|NP_037328.1|:0.01004,
++gi|53765|emb|CAA40856.1|:0.01133)
++100:0.04471,
++gi|3024415|sp|O35507|PPARA_CAV:0.06881)
++100:0.02177,
++gi|19401877|gb|AAL87699.1|AF48:0.07924)
++100:0.11628,
++(
++gi|50882280|gb|AAT85615.1|:0.13020,
++gi|14994035|gb|AAK76392.1|:-0.00248)
++100:0.11211)
++100:0.04510,
++(
++(
++gi|68303294|gb|AAY89587.1|:0.24273,
++gi|24666202|ref|NP_730322.1|:0.29207)
++100:0.05743,
++(
++(
++gi|32026|emb|CAA68398.1|:0.02054,
++gi|114585739|ref|XP_001164266.:0.00169)
++85:0.02207,
++gi|109502151|ref|XP_001059459.:0.04437)
++100:0.30861)
++100:0.14445)
++100:0.04138,
++(
++gi|85376346|gb|ABC70398.1|:0.14816,
++gi|16304880|emb|CAC95230.1|:0.21548)
++74:0.01669)
++100:0.08347,
++gi|13311191|emb|CAC34402.1|:0.08993)
++100:0.07117,
++(
++(
++(
++gi|6755138|ref|NP_035276.1|:0.00295,
++gi|454001|gb|AAC52134.1|:-0.00295)
++60:0.00339,
++gi|14627168|gb|AAG60685.2|:0.00503)
++85:0.00763,
++gi|22003526|gb|AAM88773.1|:0.01343)
++34:0.00198)
++22:0.00163,
++gi|66471842|emb|CAD91388.1|:0.06787,
++gi|47678881|dbj|BAD20642.1|:0.00789)TRICHOTOMY;
+--- treeviewx-0.5.1.orig/debian/README.Debian
++++ treeviewx-0.5.1/debian/README.Debian
+@@ -0,0 +1,7 @@
++TreeView X for Debian
++---------------------
++
++The original source code was modified by wrapping some character chains with
++wxT(), in order to build it with wxGTK 2.6. 
++
++ -- Charles Plessy <charles-debian-nospam@plessy.org>, Sat, 11 Feb 2006 17:27:26 +0900
+--- treeviewx-0.5.1.orig/debian/tv.1
++++ treeviewx-0.5.1/debian/tv.1
+@@ -0,0 +1,51 @@
++.\"     Title: TREEVIEW X
++.\"    Author: 
++.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
++.\"      Date: 01/12/2008
++.\"    Manual: 
++.\"    Source: 
++.\"
++.TH "TREEVIEW X" "1" "01/12/2008" "" ""
++.\" disable hyphenation
++.nh
++.\" disable justification (adjust text to left margin only)
++.ad l
++.SH "NAME"
++tv - displays and prints phylogenetic trees
++.SH "SYNOPSIS"
++.HP 3
++\fBtv\fR [\fIfilename\fR]
++.SH "DESCRIPTION"
++.PP
++\fBtv\fR
++is the program that starts the TreeView X GUI\.
++.PP
++TreeView X is an open source and multi\-platform program to display phylogenetic trees\. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE\-PUZZLE, and other programs)\. It allows to order the branches of the trees, and to export the trees in SVG format\.
++.PP
++If started from the command line with
++\fIfilename\fR
++as an argument, TreeView X will open the tree stored in
++\fIfilename\fR\.
++.SH "SEE ALSO"
++.PP
++At present there is is no documentation for TreeView X\. In the meantime please see the online documentation for TreeView (remember that TreeView X has only a subset of the features of TreeView)\. http://taxonomy\.zoology\.gla\.ac\.uk/rod/treeview/treeview_manual\.html
++.SH "REFERENCE"
++.PP
++Page, R\. D\. M\. 1996\. TREEVIEW: An application to display phylogenetic trees on personal computers\. Computer Applications in the Biosciences 12: 357\-358\.
++.SH "AUTHOR"
++.PP
++TreeView X
++was written by Rod Page (r\.page@bio\.gla\.ac\.uk) URL: http://darwin\.zoology\.gla\.ac\.uk/~rpage/treeviewx\.
++.PP
++This manual page was written by Charles Plessy (<charles\-debian\-nospam@plessy\.org>) for the
++Debian(TM)
++system (but may be used by others)\.
++.PP
++Permission is granted to copy, distribute and/or modify TreeView\ X and this document under the terms of the
++GNU
++General Public License, Version 2 or any later version published by the Free Software Foundation\.
++.PP
++On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\.
++.SH "COPYRIGHT"
++Copyright \(co 2006, 2008 Charles Plessy
++.br
+--- treeviewx-0.5.1.orig/debian/changelog
++++ treeviewx-0.5.1/debian/changelog
+@@ -0,0 +1,96 @@
++treeviewx (0.5.1-7) unstable; urgency=low
++
++  * Refreshed debian/copyright according to latest developments
++    of the machine-readable format.
++  * Collected upstream information in debian/upstream-metadata.yaml
++    and removed bibliographic information from the long description
++    (debian/control).
++  * Added in ‘debian/patches/90_fix_for_wx2.8.diff’ Ryan Niebur's patch
++    to build TreeView X with wxWidgets 2.8 (Closes: #567238, thanks!).
++  * Build against libwxgtk2.8-dev (debian/control).
++  * Checked conformance with Policy 3.8.4 and incremented Standards-Version
++    to reflect this (debian/control, no changes needed).
++
++ -- Charles Plessy <plessy@debian.org>  Thu, 28 Jan 2010 18:52:23 +0900
++
++treeviewx (0.5.1-6) unstable; urgency=low
++
++  [ Charles Plessy ]
++  * Updated my email address.
++
++  [ David Paleino ]
++  * Removed myself from Uploaders
++
++  [ Andreas Tille ]
++  * Standards-Version: 3.8.3 (Added README.source)
++  * debhelper 7
++  * Added myself to uploaders
++  * Tested whether package also build against libwxgtk2.8-dev but failed
++    -> Upstream should be contacted about wxgtk upgrade to be safe for
++       the future
++  * Removed explicit dependency from libgnomeprintui2.2-0
++    Closes: #542579
++
++ -- Andreas Tille <tille@debian.org>  Tue, 01 Sep 2009 11:18:11 +0200
++
++treeviewx (0.5.1-5) unstable; urgency=low
++
++  [ Charles Plessy ]
++  * Debian Menu transition: Apps/Science becomes Applications/Science/Biology.
++  * debian/control:
++    - Moved the Homepage: field out from the package's description.
++    - Checked conformance with policy 3.7.3
++    - Allowed upload by Debian Maintainers.
++  * MIME support:
++    - debian/treeviewx.sharedmimeinfo declares that .phb and .ph files are
++      Clustal W phylogenetic trees.
++    - debian/treeviewx.mime and debian/treeviewx.desktop declare that
++      TreeView X can open Clustal W phylogenetic trees.
++    - debian/rules calls dh_installmime.
++  * debian/copyright: made machine-parsable.
++  * Relicensed the manpage under "same as TreeView X" terms.
++  * Switched to CDBS and quilt.
++
++  [ David Paleino ]
++  * Added support for MIME types (.phb is now associated to treeviewx)
++  * fixed FTBFS with GCC 4.3: missing #includes (Closes: #455177)
++  * Added statically generated tv.1 (to save buildd time)
++  * Other minor fixes
++  * Added Italian to the .desktop file
++
++ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat, 26 Jan 2008 22:32:36 +0900
++
++treeviewx (0.5.1-4) unstable; urgency=low
++
++  * Add Subversion repository URL to debian/control.
++  * Including /usr/share/dpatch/dpatch.make in debian/rules.
++  * Including a patch from Martin Michlmayr to build TreeView X
++    with gcc 4.3 (Closes: #417729).
++
++ -- Charles Plessy <charles-debian-nospam@plessy.org>  Mon,  9 Apr 2007 10:03:14 +0900
++
++treeviewx (0.5.1-3) unstable; urgency=low
++
++  [ William Alexander Grant ]
++  * Added 70_choose_tree.dpatch, prevents segfault when choosing no tree.
++
++  [ Charles Plessy ]
++  * Tested and imported the patch from Ubuntu. Thanks William !
++
++ -- Charles Plessy <charles-debian-nospam@plessy.org>  Tue, 13 Feb 2007 23:38:33 +0900
++
++treeviewx (0.5.1-2) unstable; urgency=low
++
++  * Added a transitional dependency on libgnomeprintui2.2-0, thanks to Roger
++    Leigh for understanding the problem. Closes: #392219
++  * Fixed the debian/watch file.
++  * Added an example tree (courtesy of Roger Leigh).
++
++ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat, 14 Oct 2006 12:16:21 +0900
++
++treeviewx (0.5.1-1) unstable; urgency=low
++
++  * Initial release Closes: #352506
++
++ -- Charles Plessy <charles-debian-nospam@plessy.org>  Thu, 16 Mar 2006 11:30:23 +0900
++
+--- treeviewx-0.5.1.orig/debian/compat
++++ treeviewx-0.5.1/debian/compat
+@@ -0,0 +1 @@
++7
+--- treeviewx-0.5.1.orig/debian/examples
++++ treeviewx-0.5.1/debian/examples
+@@ -0,0 +1 @@
++debian/tree.phb
+--- treeviewx-0.5.1.orig/debian/install
++++ treeviewx-0.5.1/debian/install
+@@ -0,0 +1 @@
++debian/treeviewx.desktop	/usr/share/applications/
+--- treeviewx-0.5.1.orig/debian/patches/series
++++ treeviewx-0.5.1/debian/patches/series
+@@ -0,0 +1,7 @@
++45_gcc4.3.diff
++50_wxT_tv.cpp.diff
++51_wxT_tview.cpp.diff
++60_LGPLtoGPL.diff
++70_choose_tree.diff
++80_missing_includes.diff
++90_fix_for_wx2.8.diff
+--- treeviewx-0.5.1.orig/debian/patches/51_wxT_tview.cpp.diff
++++ treeviewx-0.5.1/debian/patches/51_wxT_tview.cpp.diff
+@@ -0,0 +1,25 @@
++Adding wxT escapes in the tview.cpp file
++--- tv-0.5.1-old/tview.cpp	2005-08-31 17:55:13.000000000 +0900
+++++ tv-0.5.1/tview.cpp	2006-03-13 09:35:50.000000000 +0900
++@@ -184,8 +184,8 @@
++ 	wxString pictureFileName = GetFrame()->GetTitle();
++ 	pictureFileName += wxT(".emf");
++ 	wxFrame *f = GetMainFrame();
++-   	wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
++-        "Enhanced metafile (*.emf)|*.emf",
+++   	wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName,
+++        wxT("Enhanced metafile (*.emf)|*.emf"),
++         wxSAVE|wxOVERWRITE_PROMPT);
++     
++     if (dialog.ShowModal() == wxID_OK)
++@@ -204,8 +204,8 @@
++ 	#else
++ 	wxFrame *f = GetMainFrame();
++ 	#endif 
++-    wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
++-        "SVG vector picture files (*.svg)|*.svg",
+++    wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName,
+++        wxT("SVG vector picture files (*.svg)|*.svg"),
++         wxSAVE|wxOVERWRITE_PROMPT);
++ 
++     if (dialog.ShowModal() == wxID_OK)
+--- treeviewx-0.5.1.orig/debian/patches/90_fix_for_wx2.8.diff
++++ treeviewx-0.5.1/debian/patches/90_fix_for_wx2.8.diff
+@@ -0,0 +1,15 @@
++Author: Ryan Niebur
++Bug-Debian: http://bugs.debian.org/567238
++Description: To build with wxwidgets 2.8
++Forwarded: Roderic Page <r.page@bio.gla.ac.uk>
++--- treeviewx-0.5.1.orig/tview.cpp
+++++ treeviewx-0.5.1/tview.cpp
++@@ -994,7 +994,7 @@
++ MyCanvas::MyCanvas(wxView *v, wxMDIChildFrame *frame, const wxPoint& pos, const wxSize& size, long style):
++  wxScrolledWindow(frame, -1, pos, size, style)
++ {
++-	SetBackgroundColour(wxColour("WHITE"));
+++	SetBackgroundColour(wxColour(wxT("WHITE")));
++ 	view = v;
++ 	magnification = 1;
++ }
+--- treeviewx-0.5.1.orig/debian/patches/80_missing_includes.diff
++++ treeviewx-0.5.1/debian/patches/80_missing_includes.diff
+@@ -0,0 +1,71 @@
++80_strlen_charactersblock.cpp.dpatch by David Paleino <d.paleino@gmail.com>
++Fixes "error: ‘strlen’ was not declared in this scope" during compilation
++diff -urNad trunk~/TreeLib/Parse.cpp trunk/TreeLib/Parse.cpp
++--- trunk~/TreeLib/Parse.cpp	2007-11-18 14:39:17.000000000 +0100
+++++ trunk/TreeLib/Parse.cpp	2007-11-18 14:39:18.000000000 +0100
++@@ -19,8 +19,9 @@
++  */
++ 
++  // $Id: Parse.cpp,v 1.9 2002/02/23 12:22:32 rdmp1c Exp $
++- 
+++
++ #include <ctype.h>
+++#include <cstring>
++ #include "Parse.h"
++ 
++ // Return the next token in the string
++diff -urNad trunk~/TreeLib/treereader.cpp trunk/TreeLib/treereader.cpp
++--- trunk~/TreeLib/treereader.cpp	2007-11-18 14:39:17.000000000 +0100
+++++ trunk/TreeLib/treereader.cpp	2007-11-18 14:39:36.000000000 +0100
++@@ -22,6 +22,7 @@
++ 
++ #include "treereader.h"
++ #include <cstdlib>
+++#include <cstring>
++ 
++ #if __MWERKS__
++ 	#include <string.h>
++diff -urNad trunk~/ncl-2.0/src/charactersblock.cpp trunk/ncl-2.0/src/charactersblock.cpp
++--- trunk~/ncl-2.0/src/charactersblock.cpp	2007-11-18 14:14:43.000000000 +0100
+++++ trunk/ncl-2.0/src/charactersblock.cpp	2007-11-18 14:39:18.000000000 +0100
++@@ -8,6 +8,7 @@
++ #include "discretematrix.h"
++ #include "assumptionsblock.h"
++ #include "charactersblock.h"
+++#include <cstring>
++ 
++ using namespace std;
++ 
++diff -urNad trunk~/ncl-2.0/src/nexus.cpp trunk/ncl-2.0/src/nexus.cpp
++--- trunk~/ncl-2.0/src/nexus.cpp	2007-10-02 09:51:43.000000000 +0200
+++++ trunk/ncl-2.0/src/nexus.cpp	2007-11-18 14:39:18.000000000 +0100
++@@ -2,6 +2,7 @@
++ #include "xnexus.h"
++ #include "nexustoken.h"
++ #include "nexus.h"
+++#include <cstring>
++ 
++ #define NCL_NAME_AND_VERSION  "NCL version 2.01"
++ #define NCL_COPYRIGHT         "Copyright (c) 2000 by Paul O. Lewis"
++diff -urNad trunk~/ncl-2.0/src/nexustoken.cpp trunk/ncl-2.0/src/nexustoken.cpp
++--- trunk~/ncl-2.0/src/nexustoken.cpp	2007-10-02 09:51:43.000000000 +0200
+++++ trunk/ncl-2.0/src/nexustoken.cpp	2007-11-18 14:39:18.000000000 +0100
++@@ -1,6 +1,7 @@
++ #include "nexusdefs.h"
++ #include "xnexus.h"
++ #include "nexustoken.h"
+++#include <cstring>
++ 
++ using namespace std;
++ 
++diff -urNad trunk~/ncl-2.0/src/nxsstring.cpp trunk/ncl-2.0/src/nxsstring.cpp
++--- trunk~/ncl-2.0/src/nxsstring.cpp	2007-10-02 09:51:43.000000000 +0200
+++++ trunk/ncl-2.0/src/nxsstring.cpp	2007-11-18 14:39:18.000000000 +0100
++@@ -20,6 +20,7 @@
++ #include <stdio.h>
++ #include <assert.h>
++ #include <math.h>
+++#include <cstring>
++ #include "nxsstring.h"
++ 
++ nxsstring& nxsstring::operator+=( const double d )
+--- treeviewx-0.5.1.orig/debian/patches/70_choose_tree.diff
++++ treeviewx-0.5.1/debian/patches/70_choose_tree.diff
+@@ -0,0 +1,13 @@
++## 70_choose_tree.dpatch by William Alexander Grant <william.grant@ubuntu.com.au>
++diff -urNad treeviewx-0.5.1~/tview.cpp treeviewx-0.5.1/tview.cpp
++--- treeviewx-0.5.1~/tview.cpp	2006-12-17 10:33:21.000000000 +1100
+++++ treeviewx-0.5.1/tview.cpp	2006-12-17 10:33:53.000000000 +1100
++@@ -742,7 +742,7 @@
++ 
++     dialog.SetSelection(p.GetCurrentTreeNumber());
++ 
++-    if (dialog.ShowModal() == wxID_OK)
+++    if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0))
++     {
++ 		int j = dialog.GetSelection ();				
++ #ifdef __WXMAC__
+--- treeviewx-0.5.1.orig/debian/patches/60_LGPLtoGPL.diff
++++ treeviewx-0.5.1/debian/patches/60_LGPLtoGPL.diff
+@@ -0,0 +1,1067 @@
++Converts LGPL statements to GPL, updates FSF's adress.
++diff -ruN tv.orig/COPYING tv/COPYING
++--- tv.orig/COPYING	2006-06-12 21:11:38.000000000 +0900
+++++ tv/COPYING	2006-06-28 20:39:19.000000000 +0900
++@@ -2,7 +2,7 @@
++ 		       Version 2, June 1991
++ 
++  Copyright (C) 1989, 1991 Free Software Foundation, Inc.
++-     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+++	51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
++  Everyone is permitted to copy and distribute verbatim copies
++  of this license document, but changing it is not allowed.
++ 
++@@ -305,7 +305,7 @@
++ 
++     You should have received a copy of the GNU General Public License
++     along with this program; if not, write to the Free Software
++-    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+++    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++ 
++ 
++ Also add information on how to contact you by electronic and paper mail.
++diff -ruN tv.orig/LGPLtoGPL.diff tv/LGPLtoGPL.diff
++--- tv.orig/LGPLtoGPL.diff	1970-01-01 09:00:00.000000000 +0900
+++++ tv/LGPLtoGPL.diff	2006-06-28 20:48:52.000000000 +0900
++@@ -0,0 +1,21 @@
+++diff -ruN tv.orig/COPYING tv/COPYING
+++--- tv.orig/COPYING	2006-06-12 21:11:38.000000000 +0900
++++++ tv/COPYING	2006-06-28 20:39:19.000000000 +0900
+++@@ -2,7 +2,7 @@
+++ 		       Version 2, June 1991
+++ 
+++  Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+++-     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
++++	51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+++  Everyone is permitted to copy and distribute verbatim copies
+++  of this license document, but changing it is not allowed.
+++ 
+++@@ -305,7 +305,7 @@
+++ 
+++     You should have received a copy of the GNU General Public License
+++     along with this program; if not, write to the Free Software
+++-    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
++++    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+++ 
+++ 
+++ Also add information on how to contact you by electronic and paper mail.
++diff -ruN tv.orig/tdoc.cpp tv/tdoc.cpp
++--- tv.orig/tdoc.cpp	2006-06-12 21:11:38.000000000 +0900
+++++ tv/tdoc.cpp	2006-06-28 20:30:56.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tdoc.cpp,v 1.6 2001/07/25 10:37:06 rdmp1c Exp $
++diff -ruN tv.orig/tdoc.h tv/tdoc.h
++--- tv.orig/tdoc.h	2006-06-28 20:26:50.000000000 +0900
+++++ tv/tdoc.h	2006-06-28 20:24:07.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tdoc.h,v 1.4 2001/07/24 10:49:48 rdmp1c Exp $
++diff -ruN tv.orig/tproject.h tv/tproject.h
++--- tv.orig/tproject.h	2006-06-12 21:11:38.000000000 +0900
+++++ tv/tproject.h	2006-06-28 20:30:40.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tproject.h,v 1.9 2005/08/31 08:55:25 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/lcaquery.h tv/TreeLib/lcaquery.h
++--- tv.orig/TreeLib/lcaquery.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/lcaquery.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: lcaquery.h,v 1.1 2002/03/14 14:11:42 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/mast.cpp tv/TreeLib/mast.cpp
++--- tv.orig/TreeLib/mast.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/mast.cpp	2006-06-28 20:31:07.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: mast.cpp,v 1.5 2005/05/24 22:55:16 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/mast.h tv/TreeLib/mast.h
++--- tv.orig/TreeLib/mast.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/mast.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: mast.h,v 1.1 2002/05/16 16:07:32 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/nodeiterator.h tv/TreeLib/nodeiterator.h
++--- tv.orig/TreeLib/nodeiterator.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/nodeiterator.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: nodeiterator.h,v 1.5 2005/03/29 16:48:52 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/Parse.cpp tv/TreeLib/Parse.cpp
++--- tv.orig/TreeLib/Parse.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/Parse.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: Parse.cpp,v 1.9 2002/02/23 12:22:32 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/Parse.h tv/TreeLib/Parse.h
++--- tv.orig/TreeLib/Parse.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/Parse.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: Parse.h,v 1.7 2004/03/04 23:22:42 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/profile.h tv/TreeLib/profile.h
++--- tv.orig/TreeLib/profile.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/profile.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: profile.h,v 1.30 2005/08/31 08:55:59 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/quartet.cpp tv/TreeLib/quartet.cpp
++--- tv.orig/TreeLib/quartet.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/quartet.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: quartet.cpp,v 1.2 2002/03/14 16:37:13 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/quartet.h tv/TreeLib/quartet.h
++--- tv.orig/TreeLib/quartet.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/quartet.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: quartet.h,v 1.1 2002/03/14 14:11:42 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/tokeniser.cpp tv/TreeLib/tokeniser.cpp
++--- tv.orig/TreeLib/tokeniser.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/tokeniser.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++ // $Id: tokeniser.cpp,v 1.14 2005/09/05 07:44:48 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/tokeniser.h tv/TreeLib/tokeniser.h
++--- tv.orig/TreeLib/tokeniser.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/tokeniser.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tokeniser.h,v 1.14 2003/09/17 13:05:57 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/treedrawer.cpp tv/TreeLib/treedrawer.cpp
++--- tv.orig/TreeLib/treedrawer.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treedrawer.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++ // $Id: treedrawer.cpp,v 1.18 2005/09/06 13:00:14 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/treedrawer.h tv/TreeLib/treedrawer.h
++--- tv.orig/TreeLib/treedrawer.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treedrawer.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++ // $Id: treedrawer.h,v 1.8 2004/03/16 07:07:40 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/TreeLib.cpp tv/TreeLib/TreeLib.cpp
++--- tv.orig/TreeLib/TreeLib.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/TreeLib.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++ // $Id: TreeLib.cpp,v 1.26 2004/05/13 12:22:11 jcotton Exp $
++diff -ruN tv.orig/TreeLib/TreeLib.h tv/TreeLib/TreeLib.h
++--- tv.orig/TreeLib/TreeLib.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/TreeLib.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++ // $Id: TreeLib.h,v 1.26 2004/05/13 12:22:11 jcotton Exp $
++diff -ruN tv.orig/TreeLib/treeorder.cpp tv/TreeLib/treeorder.cpp
++--- tv.orig/TreeLib/treeorder.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treeorder.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++ // $Id: treeorder.cpp,v 1.2 2005/02/23 14:19:00 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/treeorder.h tv/TreeLib/treeorder.h
++--- tv.orig/TreeLib/treeorder.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treeorder.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++ 
++  // $Id: treeorder.h,v 1.4 2005/02/23 14:19:00 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/treereader.cpp tv/TreeLib/treereader.cpp
++--- tv.orig/TreeLib/treereader.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treereader.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/treereader.h tv/TreeLib/treereader.h
++--- tv.orig/TreeLib/treereader.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treereader.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++ // $Id: treereader.h,v 1.4 2003/10/21 10:58:45 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/treewriter.cpp tv/TreeLib/treewriter.cpp
++--- tv.orig/TreeLib/treewriter.cpp	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treewriter.cpp	2006-06-28 20:31:08.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: treewriter.cpp,v 1.4 2005/02/23 14:32:44 rdmp1c Exp $
++diff -ruN tv.orig/TreeLib/treewriter.h tv/TreeLib/treewriter.h
++--- tv.orig/TreeLib/treewriter.h	2006-06-12 21:11:34.000000000 +0900
+++++ tv/TreeLib/treewriter.h	2006-06-28 20:31:23.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A library for manipulating phylogenetic trees.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++ // $Id: treewriter.h,v 1.5 2005/02/23 14:36:08 rdmp1c Exp $
++diff -ruN tv.orig/treeorder_dialog.cpp tv/treeorder_dialog.cpp
++--- tv.orig/treeorder_dialog.cpp	2006-06-12 21:11:38.000000000 +0900
+++++ tv/treeorder_dialog.cpp	2006-06-28 20:30:56.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++ // $Id: treeorder_dialog.cpp,v 1.2 2005/02/21 19:41:24 rdmp1c Exp $
++diff -ruN tv.orig/treeorder_dialog.h tv/treeorder_dialog.h
++--- tv.orig/treeorder_dialog.h	2006-06-12 21:11:38.000000000 +0900
+++++ tv/treeorder_dialog.h	2006-06-28 20:30:40.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++ // $Id: treeorder_dialog.h,v 1.2 2003/10/22 16:46:26 rdmp1c Exp $
++diff -ruN tv.orig/tv.cpp tv/tv.cpp
++--- tv.orig/tv.cpp	2006-06-12 21:11:38.000000000 +0900
+++++ tv/tv.cpp	2006-06-28 20:30:56.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tv.cpp,v 1.41 2005/03/23 13:30:32 rdmp1c Exp $
++diff -ruN tv.orig/tv.h tv/tv.h
++--- tv.orig/tv.h	2006-06-12 21:11:38.000000000 +0900
+++++ tv/tv.h	2006-06-28 20:29:26.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tv.h,v 1.4 2004/08/05 15:55:26 rdmp1c Exp $
++diff -ruN tv.orig/tview.cpp tv/tview.cpp
++--- tv.orig/tview.cpp	2006-06-12 21:11:38.000000000 +0900
+++++ tv/tview.cpp	2006-06-28 20:30:56.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tview.cpp,v 1.37 2005/08/31 08:55:13 rdmp1c Exp $
++diff -ruN tv.orig/tview.h tv/tview.h
++--- tv.orig/tview.h	2006-06-12 21:11:38.000000000 +0900
+++++ tv/tview.h	2006-06-28 20:30:43.000000000 +0900
++@@ -3,20 +3,19 @@
++  * A phylogenetic tree viewer.
++  * Copyright (C) 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
++  *
++- * This library is free software; you can redistribute it and/or
++- * modify it under the terms of the GNU Library General Public
++- * License as published by the Free Software Foundation; either
++- * version 2 of the License, or (at your option) any later version.
+++ * This program is free software; you can redistribute it and/or modify
+++ * it under the terms of the GNU General Public License as published by
+++ * the Free Software Foundation; either version 2 of the License, or
+++ * (at your option) any later version.
++  *
++- * This library is distributed in the hope that it will be useful,
+++ * This program is distributed in the hope that it will be useful,
++  * but WITHOUT ANY WARRANTY; without even the implied warranty of
++- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
++- * Library General Public License for more details.
+++ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+++ * GNU General Public License for more details.
++  *
++- * You should have received a copy of the GNU Library General Public
++- * License along with this library; if not, write to the Free
++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
++- * MA 02111-1307, USA.
+++ * You should have received a copy of the GNU General Public License
+++ * along with this program; if not, write to the Free Software
+++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
++  */
++  
++  // $Id: tview.h,v 1.21 2005/08/31 08:55:01 rdmp1c Exp $
+--- treeviewx-0.5.1.orig/debian/patches/50_wxT_tv.cpp.diff
++++ treeviewx-0.5.1/debian/patches/50_wxT_tv.cpp.diff
+@@ -0,0 +1,17 @@
++Adding wxT escapes in the tv.cpp file
++--- tv-0.5.1-old/tv.cpp	2005-03-23 22:30:32.000000000 +0900
+++++ tv-0.5.1/tv.cpp	2006-03-13 09:35:38.000000000 +0900
++@@ -312,11 +312,11 @@
++ 	{
++ #ifdef __WXMSW__
++ 		file_menu->AppendSeparator();
++-		file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile");
+++		file_menu->Append(SAVEAS_PICTURE_CMD, wxT("Save As Picture...")), wxT("Save picture of tree to metafile");
++ #else
++ 	#ifdef USE_SVG
++ 		file_menu->AppendSeparator();
++-		file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file");
+++		file_menu->Append(SAVEAS_PICTURE_CMD, wxT("Save As Picture...")), wxT("Save picture of tree to SVG file");
++ 	#endif
++ #endif
++ 		file_menu->AppendSeparator();
+--- treeviewx-0.5.1.orig/debian/patches/45_gcc4.3.diff
++++ treeviewx-0.5.1/debian/patches/45_gcc4.3.diff
+@@ -0,0 +1,21 @@
++Makes TreeView X buildable with gcc 4.3
++--- ./TreeLib/TreeLib.cpp~	2007-04-04 12:30:13.000000000 +0000
+++++ ./TreeLib/TreeLib.cpp	2007-04-04 12:30:19.000000000 +0000
++@@ -23,6 +23,7 @@
++ #include "TreeLib.h"
++ #include "Parse.h"
++ 
+++#include <cstdlib>
++ #include <vector>
++ 
++ 
++--- ./TreeLib/treereader.cpp~	2007-04-04 12:33:15.000000000 +0000
+++++ ./TreeLib/treereader.cpp	2007-04-04 12:33:27.000000000 +0000
++@@ -21,6 +21,7 @@
++  // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $
++ 
++ #include "treereader.h"
+++#include <cstdlib>
++ 
++ #if __MWERKS__
++ 	#include <string.h>
diff --git a/academic/treeview/tv.desktop b/academic/treeview/tv.desktop
new file mode 100644
index 0000000000000..b2bdefa44caea
--- /dev/null
+++ b/academic/treeview/tv.desktop
@@ -0,0 +1,7 @@
+[Desktop Entry]
+Categories=Education;
+Exec=tv
+Icon=tv.png
+Name=TreeView
+StartupNotify=false
+Type=Application
diff --git a/academic/treeview/tv.png b/academic/treeview/tv.png
new file mode 100644
index 0000000000000..fbdf9d2fcc9a3
--- /dev/null
+++ b/academic/treeview/tv.png