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academic/TreeGraph: Added (A feature rich phylogenetic tree editor).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
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academic/TreeGraph/README
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academic/TreeGraph/README
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TreeGraph (2): A feature rich and easy to use phylogenetic tree editor
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TreeGraph (2) is a is graphical editor for phylogenetic trees, which
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allows to apply various of graphical formats and edit operations and
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supports several (visible or invisible) annotations attached to nodes
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or branches. Data can be imported from many tree formats, tables and
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BayesTraits output.
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A key feature is the interactive comparison and combination of
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alternative topologies from different analyses.
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Key features
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- Read trees in Newick, Nexus format (including annotations in hot
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comments), NeXML or PhyloXML
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- Import annotations from text files or combine information from
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different phylogenetic analyses
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- An unlimited number of numerical or textual annotations on every
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branch
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- Export trees to various vector and (anti-aliased) pixel graphic
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formats (e.g. PDF, SVG, EMF or PNG)
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- Many global and element specific formats like line width or color
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and text formats
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- Versatile editing and formatting options, such as automatically
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setting branch widths or colors according to the value of any
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attached data
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- Editing operations like rerooting, ladderizing or moving and
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collapsing nodes or copying or manually creating whole clades
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- Generate commands and import data for ancestral state reconstruction
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Citation
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TreeGraph 2 has been published in BMC Bioinformatics:
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Stöver BC, Müller KF: TreeGraph 2: Combining and visualizing evidence
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from different phylogenetic analyses. BMC Bioinformatics 2010, 11:7
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DOI: 10.1186/1471-2105-11-7
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IMPORTANT NOTE ABOUT THE DOWNLOAD
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If you have trouble with the download, please use a browser to visit
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the TreeGraph download page at http://treegraph.bioinfweb.info/Download
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and click the download link.
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4
academic/TreeGraph/TreeGraph
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academic/TreeGraph/TreeGraph
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#!/bin/sh
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cd /usr/share/java/TreeGraph
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java -jar TreeGraph.jar &
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80
academic/TreeGraph/TreeGraph.SlackBuild
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academic/TreeGraph/TreeGraph.SlackBuild
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#!/bin/sh
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# Slackware build script for TreeGraph
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# Copyright 2018 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=TreeGraph
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VERSION=${VERSION:-2.14.0_771_beta}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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ZIPVER=2.14.0-771_beta
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ARCH=noarch
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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mkdir -p $PRGNAM-$VERSION
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cd $PRGNAM-$VERSION
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# Use "bsdtar" instead of "unzip". The latter has some bug which
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# prevented the script from running past the unzipping step. Or maybe
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# I did sth wrong here...
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bsdtar -xf $CWD/${PRGNAM}_${ZIPVER}.zip
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# There are a bunch of LICENSE-* txt files, however leave them there,
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# otherwise the program will fail to start. I tried moving them to
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# $PKG/usr/doc/$PRGNAM-$VERSION and had an error message upon start.
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mkdir -p $PKG/usr/share/java/$PRGNAM/lib/{batik,errorReporter}
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cp -a icons lib $PRGNAM.jar $PKG/usr/share/java/$PRGNAM
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# Install our simple wrapper
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install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM
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# Include our own icon and desktop file
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mkdir -p $PKG/usr/share/{applications,pixmaps}
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cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
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cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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academic/TreeGraph/TreeGraph.desktop
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academic/TreeGraph/TreeGraph.desktop
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[Desktop Entry]
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Categories=Education;
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Comment=A feature rich and easy to use phylogenetic tree editor
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Exec=TreeGraph
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Icon=TreeGraph
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Name=TreeGraph 2
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StartupNotify=false
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Type=Application
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academic/TreeGraph/TreeGraph.info
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academic/TreeGraph/TreeGraph.info
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PRGNAM="TreeGraph"
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VERSION="2.14.0_771_beta"
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HOMEPAGE="http://treegraph.bioinfweb.info/"
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DOWNLOAD="http://treegraph.bioinfweb.info/Download/Complete/TreeGraph_2.14.0-771_beta.zip"
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MD5SUM="78dbfd08f946bb46622314457a25a78e"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="jdk"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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BIN
academic/TreeGraph/TreeGraph.png
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BIN
academic/TreeGraph/TreeGraph.png
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After Width: | Height: | Size: 10 KiB |
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academic/TreeGraph/doinst.sh
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academic/TreeGraph/doinst.sh
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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
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fi
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19
academic/TreeGraph/slack-desc
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academic/TreeGraph/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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TreeGraph: TreeGraph (A feature rich phylogenetic tree editor)
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TreeGraph:
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TreeGraph: TreeGraph 2 is a is graphical editor for phylogenetic trees,
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TreeGraph: which allows to apply various of graphical formats and edit
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TreeGraph: operations and supports several annotations attached to nodes
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TreeGraph: or branches. Data can be imported from many tree formats,
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TreeGraph: tables and BayesTraits output. A key feature is the interactive
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TreeGraph: comparison and combination of alternative topologies from
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TreeGraph: different analyses.
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TreeGraph:
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TreeGraph: http://treegraph.bioinfweb.info/
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