update for BEAST v2.7.0 release

CompEvol · Sep 5, 2022 · 00364f0 · 00364f0
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diff --git a/_pages/download-linux-with-jre.html → _pages/download-linux-aarch64.html b/_pages/download-linux-with-jre.html → _pages/download-linux-aarch64.html
@@ -1,24 +1,25 @@
 ---
 layout: site
-title: BEAST Linux Download with JRE
+title: BEAST Linux Download 
 tags: []
 ---
 
 
 <h2>Downloading BEAST for Linux</h2>
 <p>The BEAST Download should be under way.
-<p>Once the file is downloaded, uncompress the file (<code>tar fxz BEAST_with_JRE.v2.6.7.Linux.tgz</code>) which creates a <code>beast</code> directory.
+<p>Once the file is downloaded, uncompress the file (<code>tar fxz BEAST.v2.7.0.Linux.aarch64.tgz</code>) which creates a <code>beast</code> directory.
 <p>Start BEAST, BEAUti or the other programs from a terminal using any of the scripts in <code>beast/bin</code>.
 
 <h2>Trouble shooting</h2>
 <h3>Starting issues</h3>
-<p> BEAST requires Java version 8 or higher, which you can get from your package manager, or from Adopt, e.g <a href="https://adoptopenjdk.net/">here</a>.
+<p> This version of BEAST has a java runtime included for ARM processors (like Apple's M1)
+If you run on an x86 processors (most Intel and AMD CPUs), consider using the x86 version of BEAST insteaad.</a>.
 
 <h3>Download issues</h3>
 <p>If the download failed, you can always get it from the <a href="https://github.com/CompEvol/beast2/releases">release page</a>.
 
 <script>
 window.onload = function () { 
-	window.location="https://github.com/CompEvol/beast2/releases/download/v2.6.7/BEAST_with_JRE.v2.6.7.Linux.tgz"
+	window.location="https://github.com/CompEvol/beast2/releases/download/v2.7.0/BEAST.v2.7.0.Linux.aarch64.tgz"
 }
 </script>
diff --git a/_pages/download-linux.html → _pages/download-linux-x86.html b/_pages/download-linux.html → _pages/download-linux-x86.html
@@ -7,18 +7,19 @@
 
 <h2>Downloading BEAST for Linux</h2>
 <p>The BEAST Download should be under way.
-<p>Once the file is downloaded, uncompress the file (<code>tar fxz BEAST.v2.6.7.Linux.tgz</code>) which creates a <code>beast</code> directory.
+<p>Once the file is downloaded, uncompress the file (<code>tar fxz BEAST.v2.7.0.Linux.x86.tgz</code>) which creates a <code>beast</code> directory.
 <p>Start BEAST, BEAUti or the other programs from a terminal using any of the scripts in <code>beast/bin</code>.
 
 <h2>Trouble shooting</h2>
 <h3>Starting issues</h3>
-<p> BEAST requires Java version 8 or higher, which you can get from your package manager, or from Adopt, e.g <a href="https://adoptopenjdk.net/">here</a>.
+<p> This version of BEAST has a java runtime included for x86 processors (most Intel and AMD CPUs). 
+If you run on an ARM processor, consider using the aarch64 version of BEAST insteaad.</a>.
 
 <h3>Download issues</h3>
 <p>If the download failed, you can always get it from the <a href="https://github.com/CompEvol/beast2/releases">release page</a>.
 
 <script>
 window.onload = function () { 
-	window.location="https://github.com/CompEvol/beast2/releases/download/v2.6.7/BEAST.v2.6.7.Linux.tgz"
+	window.location="https://github.com/CompEvol/beast2/releases/download/v2.7.0/BEAST.v2.7.0.Linux.x86.tgz"
 }
 </script>
diff --git a/_pages/download-mac-with-jre.html b/_pages/download-mac-with-jre.html
diff --git a/_pages/download-mac.html b/_pages/download-mac.html
@@ -10,26 +10,28 @@ <h2>Downloading BEAST for Mac</h2>
 <p>Once the file is downloaded, open the dmg file by double clicking it, and drag the BEAST folder into the Application folder in the window that pops up.
 
 <p>Start BEAST, BEAUti or the other programs by double clicking the icon in the <code>BEAST </code> directory in the Application folder.
-<p>You can also start them from a terminal using any of the scripts in <code>/Applications/BEAST v2.6.7/bin</code>.
+<p>You can also start them from a terminal using any of the scripts in <code>/Applications/BEAST v2.7.0/bin</code>.
 
 <h2>Trouble shooting</h2>
 
-<h3>BEAST on Big Sur</h3>
-<p>If there is an <a href="https://github.com/CompEvol/beast2/issues/1003">issue</a> with starting BEAST v2.6.7 on OS X Big Sur showing this message:
-<img src="https://user-images.githubusercontent.com/512538/134654992-9ff0380a-d27a-4acd-b210-90fc37c1887f.png"/>
-please download the version with the JRE included <a href="http://www.beast2.org/download-mac-with-jre/">here</a> and drag to the Applications folder.
-
-<h3>BEAST does not start</h3>
-<p>If BEAST or BEAUti does not launch, this is probably due to Java not being installed, or the default version of Java is not Java 8 or higher.
-<p>To fix this, install java, e.g. from Adopt, available <a href="https://adoptopenjdk.net/">here</a>.
-<p>On Mojave, installing later version could prevent BEAST from starting, but installing Java 8 before installing a later version seems to work</p>
-<p>&nbsp;
 <h3>Download issues</h3>
 <p>If the download failed, you can always get it from the <a href="https://github.com/CompEvol/beast2/releases">release page</a>.
 
+<h3>ARM version</h3>
+
+<p>A JRE is included in this release of BEAST based on x86 CPUs.
+	There is no ARM version of BEAST because the ARM version appeared to run considerably slower than the x86 version.
+
+<p>To create an ARM version, replace the jre directory with an ARM version of the JRE (e.g. from 
+	[Zulu azul](https://www.azul.com/downloads/?version=java-17-lts&os=macos&architecture=arm-64-bit&package=jre-fx) or 
+	[Bellsoft](https://bell-sw.com/pages/downloads/#/java-17-lts) -- make sure to select "Arm" and "Full JRE" before downloading the tar.gz version). 
+	Uncompress the tar.gz file, and move the folder to <code>/Applications/BEAST v2.7.0/jre</code>.
+	Check the file <code>/Applications/BEAST v2.7.0/jre/bin/java</code> exists.
+
+
 
 <script>
 window.onload = function () { 
-	window.location="https://github.com/CompEvol/beast2/releases/download/v2.6.7/BEAST.v2.6.7.Mac.dmg"
+	window.location="https://github.com/CompEvol/beast2/releases/download/v2.7.0/BEAST.v2.7.0.Mac.dmg"
 }
 </script>
diff --git a/_pages/download-windows-with-jre.html b/_pages/download-windows-with-jre.html
diff --git a/_pages/download-windows.html b/_pages/download-windows.html
@@ -12,12 +12,21 @@ <h2>Trouble shooting</h2>
 <h3>Download issues</h3>
 <p>If the download failed, you can always get it from the <a href="https://github.com/CompEvol/beast2/releases">release page</a>.
 
-<h3>BEAST does not start</h3>
-<p>BEAST requires Java version 8 or higher and won't start without it.
-You can get Java from Adopt, e.g <a href="https://adoptopenjdk.net/">here</a>.
+<h3>ARM version</h3>
+
+<p>A JRE is included in this release of BEAST based on x86 CPUs.
+	There is no ARM version of BEAST because the ARM version appeared to run considerably slower than the x86 version.
+
+<p>To create an ARM version, replace the jre directory with an ARM version of the JRE (e.g. from 
+	[Zulu azul](https://www.azul.com/downloads/?version=java-17-lts&os=windows&architecture=arm-64-bit&package=jre-fx) or 
+	[Bellsoft](https://bell-sw.com/pages/downloads/#/java-17-lts) -- make sure to select "Arm" and "Full JRE" before downloading the tar.gz version). 
+	Uncompress the tar.gz file, and move the folder to <code>\path\to\BEAST\jre</code>.
+	Check the file <code>\path\to\BEAST\jre\bin\java.exe</code> exists.
+
+
 
 <script>
 window.onload = function () { 
-	window.location="https://github.com/CompEvol/beast2/releases/download/v2.6.7/BEAST.v2.6.7.Windows.zip"
+	window.location="https://github.com/CompEvol/beast2/releases/download/v2.7.0/BEAST.v2.7.0.Windows.zip"
 }
 </script>
diff --git a/_posts/2022-09-01-what-is-new-in-v2.7.0.md b/_posts/2022-09-01-what-is-new-in-v2.7.0.md
@@ -0,0 +1,75 @@
+---
+layout: post
+title: What is new in v2.7.0
+tags: []
+---
+
+## BEAUti has had a facelift, allows dark mode
+
+BEAUti now uses the JavaFX library instead of Swing, which looks a bit more modern and allows themes to be changed easily.
+There are now entries under the `View` menu to choose themes, including `Dark mode`.
+
+A lot of refactoring has been required to move to the JavaFX library, so not everything is back to its old standard yet, but hopefully most of the interface is sufficiently useful.
+Do let us know by [logging an issue](https://github.com/CompEvol/BeastFX/issues) if you notice things are not working as expected.
+
+The reason for the move to JavaFX is that is allows automatic user interface testing in Java 17. 
+Automatic testing in the past has been crucial in identifying problems and without it it would not be responsible to move to Java 17 and we would be stuck with Java 8.
+
+Another consequence is that JavaFX has to be available. 
+Though expert users may be able to install both Java 17 and the corresponding correct version of JavaFX, this is a somewhat error prone and uncomfortable exercise, so BEAST is now only available packaged with Java 17.0.3 and JavaFX.
+
+
+<img alt='BEAUti v2.7.0 default' src='/images/BEAUti.v2.7.0.default.png' width="49%"/>
+<img alt='BEAUti v2.7.0 dark' src='/images/BEAUti.v2.7.0.dark.png' width="49%"/>
+
+
+## BEAUti templates reorganised for better performance
+
+BEAUti templates have been updated to include smarter operators (see "Faster MCMC convergence" below).
+Out of date templates for *BEAST and the uncorrelated relaxed clock moved to the [BEAST_CLASSIC](https://github.com/BEAST2-Dev/beast-classic/) package.
+Users are encouraged to install [StarBeast3](https://github.com/rbouckaert/starbeast3) and the [optimised relaxed clock](https://github.com/jordandouglas/ORC) (ORC) packages as replacement.
+
+## "Help me choose" buttons added to BEAUti for direct targeted help
+
+Where help is available, small help buttons are added to tabs and entries in BEAUti that link to the "[help me choose](https://beast2-dev.github.io/hmc/)" site, providing direct targeted help for the entries in the BEAUti panels. 
+At the time of writing, there are 181 help me choose pages available, mostly for the Standard and StarBeast3 templates.
+This is a living project and package developers can add more pages and link them by putting appropriate information in BEAUti templates.
+
+## Faster MCMC convergence due to smarter operators
+
+BEAUti templates have been updated to include the Tree Stretch and Epoch Flex operators   from the BICEPS package as replacement of the tree scaler for better mixing of trees.
+Standard operators are replaced by [Bactrian operator](https://www.beast2.org/2021/04/26/bactrian-proposals.html) variants where available.
+Each partition gets an adaptable variance multivariate normal (AVMN) operator that does proposals for all site model operators and potentially the mean clock rate (if only applied to that partition) and the tree scale.
+Since the AVMN operator does not always converge well, it is wrapped in a [adaptable operator](https://www.beast2.org/2021/05/24/developing-operators.html) together with the (Bactrian) standard operator for each of the parameters involved.
+Altogether, these result in better mixing of MCMC chains.
+
+## DensiTree v3.0.0 included, which allows pairwise comparison of tree sets
+
+The version of DensiTree is updated to v3.0.0, which has more node ordering heuristics, but mostly has better support for comparing two tree sets by
+
+1. Displaying two tree stes at the same time in the same DensiTree, one mirrored.
+2. Provide clade comparison panel showing the difference in clade support and clade height distributions.
+3. Allow interactive exploration by selecting clades in one of the main DensiTree, clade list or clade comparison panel, which then highlights the same clade in the other panels.
+
+<img src="/images/DensiTree.v3.0.png" alt="DensiTree v3.0"/>
+
+## Uses latest version of libraries: java 17, javafx, commons math, etc.
+
+The code has been modernised to use the latest libraries: `antlr-runtime-4.10.1.jar`, `commons-math3-3.6.1.jar`, `junit5` and of course `java17` and `javafx`.
+This allows use of [newer java features](https://en.wikipedia.org/wiki/Java_version_history) and java 17 has long term support (till September 2029).
+
+
+## Code reorganised, BEAST split into two packages: BEAST.base and BEAST.app
+
+The code is reorganised to follow a more logical java package structure.
+Furthermore, the applications (BEAST, BEAUTi, TreeAnnotator, etc.) have been split off into its own package `BEAST.app` and moved to its own repository [here](https://github.com/rbouckaert/BeastFX).
+
+
+## Module like treatment of BEAST packages to prevent package library clashes
+
+Previously, all libraries were loaded by the same class loader, which meant that if Package A uses library X version 1 and Package B uses library X version 2 it was not well defined which version of the library got loaded.
+With v2.7.0, each package can load its own version of the library without clashing.
+This means, BEAST packages for v2.6.x need to be updated to work with v2.7.0.
+Not all packages have been updated yet, but this is work in progress.
+
+
diff --git a/images/BEAUti.v2.7.0.dark.png b/images/BEAUti.v2.7.0.dark.png
diff --git a/images/BEAUti.v2.7.0.default.png b/images/BEAUti.v2.7.0.default.png
diff --git a/images/DensiTree.v3.0.png b/images/DensiTree.v3.0.png
diff --git a/index.html b/index.html
@@ -7,24 +7,23 @@
 
 <p>BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.</p>
 <h2>Download</h2>
-<p>The latest version of BEAST 2 is version 2.6.7. To install this version, 
+<p>The latest version of BEAST 2 is version 2.7.0. To install this version, 
 select one of the following  to download the version for your operating system:
 <ul>
- 	<li>Download for Windows
- 	<a id="windowsDownload" href="/download-windows/">without java (8MB)</a>
- 	/<a id="windowsDownload" href="/download-windows-with-jre/">with java (45MB)</a>	 	
+ 	<li>Download 
+ 	<a id="windowsDownload" href="/download-windows/">for Windows (90MB)</a>
 	 	</li>
- 	<li>Download for Mac OS X
- 	<a id="macDownload" href="/download-mac/">without java (8MB)</a>
- 	/<a id="macDownload" href="/download-mac-with-jre/">with java (46MB)</a>
+ 	<li>Download for 
+ 	<a id="macDownload" href="/download-mac/">Mac OS X (87MB)</a>
  		</li>
  	<li>Download for Linux
- 	<a id="linuxDownload" href="/download-linux/">without java (8MB)</a>
- 	/<a id="linuxDownload" href="/download-linux-with-jre/">with java (47MB)</a>
+ 	<a id="linuxDownload" href="/download-linux-x86/">x86 (91MB)</a>
+ 	/<a id="linuxDownload" href="/download-linux-aarch64/">aarch64 (92MB)</a>
 	 	</li>
 </ul>	 	
-<p>After this, or if you already have v2.6.X (X=0, 1 or 2) installed, you can upgrade via the package manager.</p>
-<p>If you download a version of BEAST without Java, you need to install Java separately (for OS X, <a href="https://adoptium.net/?variant=openjdk8">JDK 8</a> is recommended). BEAST requires Java version 8 or higher.
+<!--<p>
+After this, or if you already have v2.7.X (X=0, 1 or 2) installed, you can upgrade via the package manager.</p>
+-->
 Older versions are available from the <a href="https://github.com/CompEvol/beast2/releases">BEAST2 releases web page</a>.
 
 <p class="p1">The BEAST 2 source code is available from the <a href="http://www.github.com/CompEvol/beast2">GitHub repository</a>, which produces the latest cutting edge jar file here: <a href="http://hudson.cs.auckland.ac.nz/job/BEAST2/lastSuccessfulBuild/artifact/build/dist/beast.jar">beast.jar</a>. </p>