reorganise images + fix links

BEAST/index.html

@@ -11,9 +11,9 @@
 <p>Recently, a few users reported problems with BEAST 2 performance, concluding it was worse than BEAST 1. This puzzled us, because BEAST 1 and 2 share the same core algorithms, and both spend most of their time doing phylogenetic likelihood calculations, which is optimised using <a href="https://github.com/beagle-dev/beagle-lib">BEAGLE</a>, a library shared by both programs. In fact, recently we changed the way that BEAST 2 handles proportion invariant categories, saving some phylogenetic likelihood calculations, so in theory it should be faster when using a proportion of invariant sites in the model. So, we became curious whether there are real performance differences between BEAST 1 and 2 and decided to do a benchmark. We expected them to perform roughly the same on GTR and GRT+G analyses, and BEAST 2 to do better on GTR+I and GTR+G+I analyses.</p>
 <p>The picture below summarises the speed of BEAST 2 over BEAST 1 using 1, 2, 4 thread(s) in the 3 different operation systems. As you can see the performance is very similar for GTR and GTR+G, with BEAST2 being perhaps slight faster (although this could be due to debugging that BEAST1 performs at the start of the chain):<br />
 </p>
-<p><img src="../files/2016/04/1-thread-perf-all.png" alt="single thread" /></p>
-<p><img src="../files/2016/04/2-threads-perf-all.png" alt="double threads" /></p>
-<p><img src="../files/2016/04/4-threads-perf-all.png" alt="four threads" /></p>
+<p><img src="/images/1-thread-perf-all.png" alt="single thread" /></p>
+<p><img src="/images/2-threads-perf-all.png" alt="double threads" /></p>
+<p><img src="/images/4-threads-perf-all.png" alt="four threads" /></p>
 <h2>What we did</h2>
 <h3>Analyses</h3>
 <p>BEAST can do many kinds of analyses, but for the purpose of this benchmark, we want to see whether the TreeLikelihood calculations, which typically dominate the computational time of MCMC runs, are comparable. To see the impact of the way BEAST 2 handles proportion invariant, we want to have an analysis with and without a proportion invariant category. And since many analyses use gamma rate heterogeneity with and without proportion invariants, we end up with four variants:</p>
@@ -149,11 +149,11 @@ <h2>Results</h2>
 The images below show the run time for 1, 2, 4 thread(s) in Linux, where <em>1.8.3(t0)</em> presents no threading pool for single thread in BEAST 1.8.3.</p>
 <ul>
 <li>1 thread:<br />
-<img src="../files/2016/04/1-thread-linux.png" alt="1 thread Linux" /></li>
+<img src="/images/1-thread-linux.png" alt="1 thread Linux" /></li>
 <li>2 threads:<br />
-<img src="../files/2016/04/2-threads-linux.png" alt="2 threads Linux" /></li>
+<img src="/images/2-threads-linux.png" alt="2 threads Linux" /></li>
 <li>4 threads:<br />
-<img src="../files/2016/04/4-threads-linux.png" alt="4 threads Linux" /></li>
+<img src="/images/4-threads-linux.png" alt="4 threads Linux" /></li>
 </ul>
 <p>With increasing number of threads, the difference in run time in seconds decreases, but BEAST 2 is almost always slightly faster than BEAST 1 in these comparisons. However, it turned out that the data sets are too small for four threads to be of much use &#8212; the four threaded runs tended to be slower than for two threads, which is optimal for most of these datasets for both BEAST versions. This may also be a function of the hardware used.</p>
 <p>Cursory checks of ESSs for BEAST 1 and 2 in Tracer did not show any substantial difference, which is not surprising since the same mixture of operators was used. Also, parameter estimates tended to agree between some randomly selected analyses.</p>

_pages/constraints-of-monophyly.html

@@ -7,10 +7,10 @@
 
 		<h2>Using BEAUti</h2>
 <p>Constraining a clade to be monphyletic is easiest done in via <a title="BEAUti" href="/beauti/">BEAUti</a> from the &#8220;Priors&#8221; tab and selecting the &#8220;+&#8221; button at the bottom of the screen. A window is shown where you can specify the taxa of a clade and the name of the clade.</p>
-<p><img class="alignnone size-full wp-image-400" src="..//files/2015/05/TaxonSetEditor.png" alt="TaxonSetEditor" width="485" height="306"  sizes="(max-width: 485px) 100vw, 485px" /></p>
+<p><img class="alignnone size-full wp-image-400" src="/images/TaxonSetEditor.png" alt="TaxonSetEditor" width="485" height="306"  sizes="(max-width: 485px) 100vw, 485px" /></p>
 <p>&nbsp;</p>
 <p>When closing, a new entry appears in the priors panel. Click the monophyletic checkbox to ensure the clade is forced to be monophyletic.</p>
-<p><img class="alignnone size-full wp-image-401" src="..//files/2015/05/Monophyletic.png" alt="Monophyletic" width="859" height="481" sizes="(max-width: 859px) 100vw, 859px" /></p>
+<p><img class="alignnone size-full wp-image-401" src="/images/Monophyletic.png" alt="Monophyletic" width="859" height="481" sizes="(max-width: 859px) 100vw, 859px" /></p>
 <p>&nbsp;</p>
 <h2>By editing XML </h2>
 <p>Firstly create a <code>distribution</code> that contains the group you want to constrain to be monophyletic. By adding the distribution element directly to the XML inside the element with id &#8220;prior&#8221; like so:</p>

_pages/increasing-memory-usage.html

@@ -22,11 +22,11 @@ <h2>Mac OS X version</h2>
 <li>Right-click (or Control-click if you are using a 1-button mouse) on the BEAST application icon:</li>
 </ol>
 
-<p><img class="alignnone wp-image-359 size-full" src="..//files/2015/05/Rightclick.png" alt="Rightclick" width="327" height="306"  sizes="(max-width: 327px) 100vw, 327px" /></p>
+<p><img class="alignnone wp-image-359 size-full" src="/images/Rightclick.png" alt="Rightclick" width="327" height="306"  sizes="(max-width: 327px) 100vw, 327px" /></p>
 
 <p>Now go into the folder called &#8220;Contents&#8221; and find the file called &#8216;info.plist&#8217;. Double-clicking this file should open it in an application called &#8220;Property List Editor&#8221; (this can be found in your Developer/Applications/Utility folder if it doesn&#8217;t open automatically, but you will need to have installed the Developer Tools). In this program open the section called &#8220;Java&#8221; and edit the string labelled &#8220;VMOptions&#8221;:</p>
 
-<p><img class="alignnone wp-image-360 size-full" src="..//files/2015/05/Plist.png" alt="Plist" width="610" height="560"  sizes="(max-width: 610px) 100vw, 610px" /></p>
+<p><img class="alignnone wp-image-360 size-full" src="/images/Plist.png" alt="Plist" width="610" height="560"  sizes="(max-width: 610px) 100vw, 610px" /></p>
 <p>&nbsp;</p>
 
 <p>This will have the format: <code>-Xss256M -Xmx8G</code>, where the -Xmx and -Xss commands determine the maximum and starting amount of memory that java is provided (the M after each number specifies that it is in megabytes, G for gigabytes). You can now increase the -Xmx option to something larger. Then save the &#8220;info.plist&#8221; file, close the folders and try running the program again.</p>

_pages/managing-packages.html

@@ -9,21 +9,21 @@
 <p>Packages (previously known as add-ons or plugins) can be installed through BEAUti or from the command line.</p>
 <h2 id="Desktop_machines">Desktop machines </h2>
 <p>The easiest way to Manage packages and install/un-install them is to start up BEAUti and select the menu File/Manage Packages. A window pops up where you can select the packages in the list to (un)install.</p>
-<p><img class="alignnone wp-image-365 size-full" src="{{site.baseurl}}/files/2015/05/Package_manager.png" alt="Package_manager" width="690" height="457" sizes="(max-width: 690px) 100vw, 690px" /></p>
+<p><img class="alignnone wp-image-365 size-full" src="/images/Package_manager.png" alt="Package_manager" width="690" height="457" sizes="(max-width: 690px) 100vw, 690px" /></p>
 <p>BEAST 2.1.2</p>
 <p>In the example above, BDSKY, BEAST_CLASSIC, BEASTlabs, MODEL_SELECTION, RBS and SNAPP are installed, and the rest are not.</p>
-<p><img class="alignnone size-full wp-image-366" src="{{site.baseurl}}/files/2015/05/AddOnManagerDialog.png" alt="AddOnManagerDialog" width="480" height="219" sizes="(max-width: 480px) 100vw, 480px" /></p>
+<p><img class="alignnone size-full wp-image-366" src="/images/AddOnManagerDialog.png" alt="AddOnManagerDialog" width="480" height="219" sizes="(max-width: 480px) 100vw, 480px" /></p>
 <p>older versions of BEAST</p>
 <p>In the example above, SNAPP and RB are installed, and the rest are not.</p>
 <h2 id="Installation_directories">Installation directories </h2>
 <p>To see where packages are installed, click the button with question mark in the dialog&#8217;s right left corner. A new dialog is shown with the information where you can find packages. Different operating systems have different locations where the packages are installed. There is a local package directory and a system wide package directory. Packages installed through the packagemanager dialog in BEAUti are saved in the user&#8217;s local package directory. To install in the system wide directory, just move the directory with the package to the system wide package directory OR use the command line version (see below).</p>
 <p>Mac:</p>
-<p><img class="alignnone wp-image-367 size-full" src="{{site.baseurl}}/files/2015/05/AddOnManagerDialogMac.png" alt="AddOnManagerDialogMac" width="516" height="300" sizes="(max-width: 516px) 100vw, 516px" /></p>
+<p><img class="alignnone wp-image-367 size-full" src="/images/AddOnManagerDialogMac.png" alt="AddOnManagerDialogMac" width="516" height="300" sizes="(max-width: 516px) 100vw, 516px" /></p>
 <p>&nbsp;</p>
 <p>&nbsp;</p>
 <p>Linux:</p>
 <p>&nbsp;</p>
-<p><img class="alignnone size-full wp-image-368" src="{{site.baseurl}}/files/2015/05/AddOnManagerDialogLinux.png" alt="AddOnManagerDialogLinux" width="341" height="277" sizes="(max-width: 341px) 100vw, 341px" /></p>
+<p><img class="alignnone size-full wp-image-368" src="/images/AddOnManagerDialogLinux.png" alt="AddOnManagerDialogLinux" width="341" height="277" sizes="(max-width: 341px) 100vw, 341px" /></p>
 <h2 id="Server_machines">Server machines </h2>
 <p>For computers without GUI, like high performance clusters, packages can be managed through the command line. An application called &#8216;packagemanager&#8217; is part of the Linux distribution of BEAST, and has the following options:</p>
 

_pages/snapp.html

@@ -6,7 +6,7 @@
 
 
 
-<h2><img class="alignnone size-full wp-image-455" src="..//files/2015/05/Snapp.png" alt="SNAPP" width="700" height="157" sizes="(max-width: 700px) 100vw, 700px" /></h2>
+<h2><img class="alignnone size-full wp-image-455" src="/images/Snapp.png" alt="SNAPP" width="700" height="157" sizes="(max-width: 700px) 100vw, 700px" /></h2>
 <h2>Introduction </h2>
 <p>SNAPP (SNP and AFLP Package for Phylogenetic analysis) is package for inferring species trees and species demographics from independent (unlinked) biallelic markers such as well spaced SNPs. It implements a full coalescent model, but uses a novel algorithm to integrate over all possible gene trees, rather than sampling them explicitly.</p>
 <p>Like a standard BEAST analysis, a SNAPP analysis is controlled using a specially formatted XML file. This file can be created from scratch, or by using the graphical user interface in BEAUTi. After setting up the analysis in BEAUTi you can take the XML file and use it to run BEAST on any computer or server.</p>

_posts/2016-10-12-announcing-taming-the-beast-in-the-south-pacific.html

@@ -10,7 +10,7 @@
 		<p style="text-align: center;"><strong>*** Deadline extended to 7th NOVEMBER for late applications ***</strong></p>
 <p style="text-align: center;"><strong>*** Just a few places left. ***</strong></p>
 <p><a href="https://www.compevol.auckland.ac.nz/en/events/events-2017/02/beast-south-pacific-1.html">Taming the BEAST in the South Pacific</a> is a comprehensive 5-day workshop to be held on the scenic Waiheke Island, New Zealand from 5 &#8211; 10 February 2017.</p>
-<p><a href="taming-the-beast-poster_blue-mouse-e1476238690707.jpg"><img class="aligncenter size-full wp-image-1291" src="{{ site.baseurl }}/images/taming-the-beast-poster_blue-mouse-e1476238690707.jpg" alt="taming the beast poster_blue mouse" width="700" height="495" /></a></p>
+<p><a href="/images/taming-the-beast-poster_blue-mouse-e1476238690707.jpg"><img class="aligncenter size-full wp-image-1291" src="{{ site.baseurl }}/images/taming-the-beast-poster_blue-mouse-e1476238690707.jpg" alt="taming the beast poster_blue mouse" width="700" height="495" /></a></p>
 <p>This workshop will equip researchers with the skills to use BEAST2 software to perform phylogenetics and phylodynamic inferences across a wide range of disciplines through a series of talks by leading experts, lectures and hands-on tutorial sessions. Participants are also encouraged to bring their own datasets for one-on-one discussion and guidance.</p>
 <p>Speakers confirmed for the workshop are leading experts in the field:</p>
 <ul>
@@ -21,7 +21,7 @@
 <li>Tracy Heath, Iowa State University</li>
 </ul>
 <p><a href="https://www.compevol.auckland.ac.nz/en/events/events-2017/02/beast-south-pacific-1.html">Taming the BEAST in the South Pacific</a> is hosted by the <a href="http://www.compevol.auckland.ac.nz">Centre for Computational Evolution</a> at the University of Auckland, and is modelled after the Taming the BEAST summer school in the Swiss Alps which was organised by the Computational Evolution Group at ETH Zurich. <del>Registration of interest for Taming the BEAST in the South Pacific is open until 25 October 2016.</del> <strong>Deadline for late applications is 7th November 2016. Just a few places left, first in first served!</strong> See <a href="http://www.compevol.auckland.ac.nz">www.compevol.auckland.ac.nz</a> for more information and registration details. Three partial scholarships have been made available for postgraduate students.</p>
-<p style="text-align: center;"><a href="south-pacific-_black-mouse_medium.jpg"><img class="alignnone size-medium wp-image-1288" src="{{ site.baseurl }}/images/south-pacific-_black-mouse_medium-300x252.jpg" alt="south pacific _black mouse_medium" width="300" height="252"  /></a></p>
+<p style="text-align: center;"><a href="/images/south-pacific-_black-mouse_medium.jpg"><img class="alignnone size-medium wp-image-1288" src="{{ site.baseurl }}/images/south-pacific-_black-mouse_medium-300x252.jpg" alt="south pacific _black mouse_medium" width="300" height="252"  /></a></p>
 
 
 

book/index.html

@@ -5,7 +5,7 @@
 ---
 
 
-		<h2><img class=" wp-image-924 size-medium alignleft" src="../files/2015/05/BEASTCover-199x300.jpg" alt="BEASTCover" width="199" height="300" />Bayesian Evolutionary Analysis with BEAST</h2>
+		<h2><img class=" wp-image-924 size-medium alignleft" src="/images/BEASTCover-199x300.jpg" alt="BEASTCover" width="199" height="300" />Bayesian Evolutionary Analysis with BEAST</h2>
 <p><em>By Alexei J. Drummond and Remco R. Bouckaert</em></p>
 <p>The BEAST book is now available from the publisher <a href="http://www.cambridge.org/9781107019652">Cambridge University Press</a>, on <a href="https://books.google.co.nz/books?id=deHUrQEACAAJ&amp;dq=isbn:1107019656&amp;hl=en&amp;sa=X&amp;ved=0CCIQ6AEwAWoVChMI0oPOlqHfxgIVA9qmCh3GWQPP">Google books</a> and on <a href="http://www.amazon.com/dp/1107019656/">Amazon</a>.</p>
 <p>We hope you find it useful! If you have feedback please email us at: Alexei (<i><a href="mailto:[email protected]">[email protected]</a></i>) and Remco (<i><a href="mailto:[email protected]">[email protected]</a></i>)</p>