DistaClusters

Release/DistanceClusters/MacOSX/Changes.txt

@@ -0,0 +1,34 @@
+Changelog
+==========
+
+- Development
+
+- 1.7.9 
+    - Turned off displaying 'N's in the display, as we don't re-export
+      those anyway.
+    - Fixed a bug in the Cluster tool reported by Michael Balke: single
+      species without conspecific sequences in the dataset were being
+      reported as 'Split'.
+
+- 1.7.8
+    - Added DOI to the citation for Sequence Matrix.
+
+- 1.7.7-dev4
+    - Naked Nexus now replaces all non-alphanumeric characters with underscores.
+
+- 1.7.7-dev3 
+    - Fixed a minor bug with clustering in which the "% of valid comparisons
+      above the threshold" number was always 0%.
+    - Fixed a bug in which multiple "Cluster" analyses in the same session
+      caused the ProgressDialog to never close, resulting in the program
+      getting "stuck" and a forced quit becoming necessary.
+
+- 1.7.7-dev2 
+    - Rewrote SpeciesDetails to remove the old, bug-ridden algorithm.
+      The new one will probably actually work.
+    - Added discrimination between "Split only", "Lumped/Split" and
+      "Lumped" for clusters in Cluster.
+
+- 1.7.6 (June 6, 2010)
+    - Added code to detect overlapping codonsets on input (#19).
+    - Fixed a bug relating to TNT files exported into directory (#55).

Release/DistanceClusters/MacOSX/DistanceClusters.app/Contents/Info.plist

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleAllowMixedLocalizations</key>
+	<string>true</string>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>English</string>
+	<key>CFBundleExecutable</key>
+	<string>JavaApplicationStub</string>
+	<key>CFBundleIconFile</key>
+	<string>GenericJavaApp.icns</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleName</key>
+	<string>DistanceClusters</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleSignature</key>
+	<string>????</string>
+	<key>CFBundleVersion</key>
+	<string>100.0</string>
+	<key>Java</key>
+	<dict>
+		<key>ClassPath</key>
+		<string>$JAVAROOT/DtClusters.jar</string>
+		<key>JVMVersion</key>
+		<string>1.4+</string>
+		<key>MainClass</key>
+		<string>com.ggvaidya.TaxonDNA.DtClusters.DtClusters</string>
+		<key>VMOptions</key>
+		<string>-Xmx1000m</string>
+	</dict>
+</dict>
+</plist>

Release/DistanceClusters/MacOSX/DistanceClusters.app/Contents/PkgInfo

@@ -0,0 +1 @@
+APPL????

Release/DistanceClusters/Windows/Changes.txt

@@ -0,0 +1,34 @@
+Changelog
+==========
+
+- Development
+
+- 1.7.9 
+    - Turned off displaying 'N's in the display, as we don't re-export
+      those anyway.
+    - Fixed a bug in the Cluster tool reported by Michael Balke: single
+      species without conspecific sequences in the dataset were being
+      reported as 'Split'.
+
+- 1.7.8
+    - Added DOI to the citation for Sequence Matrix.
+
+- 1.7.7-dev4
+    - Naked Nexus now replaces all non-alphanumeric characters with underscores.
+
+- 1.7.7-dev3 
+    - Fixed a minor bug with clustering in which the "% of valid comparisons
+      above the threshold" number was always 0%.
+    - Fixed a bug in which multiple "Cluster" analyses in the same session
+      caused the ProgressDialog to never close, resulting in the program
+      getting "stuck" and a forced quit becoming necessary.
+
+- 1.7.7-dev2 
+    - Rewrote SpeciesDetails to remove the old, bug-ridden algorithm.
+      The new one will probably actually work.
+    - Added discrimination between "Split only", "Lumped/Split" and
+      "Lumped" for clusters in Cluster.
+
+- 1.7.6 (June 6, 2010)
+    - Added code to detect overlapping codonsets on input (#19).
+    - Fixed a bug relating to TNT files exported into directory (#55).

Release/DistanceClusters/Windows/DtClusters.bat

@@ -0,0 +1,2 @@
+@echo off
+%WINDIR%\System32\java.exe -Xmx1000M -jar DtClusters.jar

Tests/expected/output.txt

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+# Cluster stability between 1.0% and 5.0% on Fri Apr 15 16:40:38 SGT 2011 upon 1390 sequences
+Threshold	Clusters	Shared clusters
+1.0	582	NA
+2.0	503	-1
+3.0	471	-1
+4.0	438	-1
+5.0	403	-1