diff --git a/BioArchLinux/mesquite/PKGBUILD b/BioArchLinux/mesquite/PKGBUILD
index fd22b1cd45..74ec553816 100644
--- a/BioArchLinux/mesquite/PKGBUILD
+++ b/BioArchLinux/mesquite/PKGBUILD
@@ -3,38 +3,79 @@
 # Contributor: Anton Bazhenov <anton.bazhenov at gmail>
 # Contributor: Mick Elliot <micke at sfu dot ca>
 
-pkgname=mesquite
-pkgver=3\.81_build955
+pkgbase=mesquite
+pkgname=('mesquite' 'mesquite-extra' 'mesquite-doc')
+pkgver=3.81_build955
 pkgrel=1
-pkgdesc="A modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms"
 arch=('any')
 url="http://mesquiteproject.org"
 license=('LGPL')
-depends=('java-runtime=8')
-source=($pkgname-${pkgver: 0: 4}::https://github.com/MesquiteProject/MesquiteCore/releases/download/v${pkgver//_/-}/Mesquite_${pkgver: 0: 4}_Linux.tgz
-        $pkgname.png
-        $pkgname.desktop
-	$pkgname.sh
+makedepends=('java-environment=8' 'maven' 'git' 'libicns' 'gendesk')
+source=($pkgbase::git+https://github.com/MesquiteProject/MesquiteCore.git#tag=v${pkgver//_/-}
+	$pkgbase.patch::https://github.com/MesquiteProject/MesquiteCore/pull/108.patch
         )
-md5sums=('560700a0968ea4be1eb96df3674f876d'
-         '8b62ba93f95aab14a8643bf5b939f465'
-         '5107a3118443aca1eac69db381d7df50'
-         'f6ff62edbf95e40d21c7bceadb35ecfe')
+md5sums=('SKIP'
+         '530fb128307845f75633ee897715b2c3')
+prepare() {
+  cd $srcdir/$pkgbase
+  patch -p1 < $srcdir/$pkgbase.patch
+}
 
-package() {
-  cd $srcdir/Mesquite_Folder
+build() {
+  cd $srcdir/$pkgbase
+  
+  # compile pkg
+  mvn package
+  
+  # generate desktop
+  gendesk --pkgname "$pkgbase" --pkgdesc "A modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms" --exec="$pkgbase" --icon="$pkgbase"
+
+  # generate binary
+  echo "java -jar /usr/share/$pkgbase/Mesquite.jar" >> $pkgbase
+  chmod +x $pkgbase
+
+  cd target/classes
+  rm -rf *.exe Mesquite_Start* starting* Running* examples
+}
+
+package_mesquite() {
+  depends=('java-runtime=8' 'sh' 'python')
+  pkgdesc="A modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms"
+  optdepends=('mesquite-doc: doc for mesquite'
+	      'mesquite-extra: extra data for mesquite')
+  cd $srcdir/$pkgname
+  cd target/classes
 
-  # Remove bundled shell script and install own
-  rm -rf $pkgdir/$pkgname.sh
-  install -Dm755 ../$pkgname.sh $pkgdir/usr/bin/$pkgname
- 
   # Install program files
   mkdir -p $pkgdir/usr/share/$pkgname
   cp -r * $pkgdir/usr/share/$pkgname
   find $pkgdir/usr/share/$pkgname -type f -exec chmod 644 '{}' \;
 
+  # Install icons 
+  cd $srcdir/$pkgname/Executables/"MacOS via Automator and Script"
+  icns2png -x Mesquite.icns
+  install -Dm 644 Mesquite_128x128x32.png $pkgdir/usr/share/pixmaps/$pkgname.png
+
+  # install binary
+  install -Dm755 $srcdir/$pkgbase/$pkgbase $pkgdir/usr/bin/$pkgbase
 
   # Install a desktop entry
-  install -Dm644 ../$pkgname.png $pkgdir/usr/share/pixmaps/$pkgname.png
-  install -Dm644 ../$pkgname.desktop $pkgdir/usr/share/applications/$pkgname.desktop
+  install -Dm755 ${srcdir}/$pkgbase/$pkgbase.desktop $pkgdir/usr/share/applications/$pkgname.desktop
+}
+
+package_mesquite-doc(){
+  pkgdesc="doc for mesquite"
+  cd $srcdir/$pkgbase
+  mkdir -p $pkgdir/usr/share/doc/$pkgbase/
+  mv docs/* $pkgdir/usr/share/doc/$pkgbase/
+  mkdir -p $pkgdir/usr/share/$pkgbase/
+  ln -s /usr/share/doc/$pkgbase $pkgdir/usr/share/$pkgbase/docs
+}
+
+package_mesquite-extra(){
+  pkgdesc="extra data for mesquite"
+  cd $srcdir/$pkgbase
+  mkdir -p $pkgdir/usr/share/$pkgbase/
+  cd Resources
+  mv examples $pkgdir/usr/share/$pkgbase/
 }
diff --git a/BioArchLinux/mesquite/mesquite.desktop b/BioArchLinux/mesquite/mesquite.desktop
deleted file mode 100644
index 4ae7017801..0000000000
--- a/BioArchLinux/mesquite/mesquite.desktop
+++ /dev/null
@@ -1,9 +0,0 @@
-[Desktop Entry]
-Type=Application
-Version=1.0
-Name=Mesquite
-Comment=A modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms.
-Exec=mesquite %U
-Icon=mesquite
-Terminal=false
-Categories=Java;Education;Science;Biology;
diff --git a/BioArchLinux/mesquite/mesquite.png b/BioArchLinux/mesquite/mesquite.png
deleted file mode 100644
index 620884c21a..0000000000
Binary files a/BioArchLinux/mesquite/mesquite.png and /dev/null differ
diff --git a/BioArchLinux/mesquite/mesquite.sh b/BioArchLinux/mesquite/mesquite.sh
deleted file mode 100644
index cdf631a38d..0000000000
--- a/BioArchLinux/mesquite/mesquite.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh
-java=/usr/bin/java
-dir=/usr/share/mesquite
-
-cp -r  "$dir/../Resources/com/"* "$dir/com/" >& /dev/null
-$java -Djava.library.path=lib -Djri.ignore.ule="yes" -cp "$dir" mesquite.Mesquite $*
-
-