# HG changeset patch
# User jasper
# Date 1486153601 18000
# Node ID 661b74ba4cc8a3b172c6e05682f1db274f683899
# Parent 2040cda75d1fb1744661eb7784a5dc89e8f5627b
Uploaded
diff -r 2040cda75d1f -r 661b74ba4cc8 cluster-picker.xml
--- a/cluster-picker.xml Tue Jan 24 14:09:46 2017 -0500
+++ b/cluster-picker.xml Fri Feb 03 15:26:41 2017 -0500
@@ -3,12 +3,14 @@
cluster-picker
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@@ -35,20 +37,37 @@
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Cluster identification strategies differ between studies and as a consequence cluster definitions vary.
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+ @ARTICLE{cluster-picker,
+ author = {Ragonnet-Cronin, Manon, et al;},
+ title = {Automated analysis of phylogenetic clusters},
+ journal = {BMC bioinformatics},
+ year = {2013},
+ volume = {14.1},
+ pages = {317}}
+
+
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/._.DS_Store
Binary file test-data/._.DS_Store has changed
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dummy.fasta Fri Feb 03 15:26:41 2017 -0500
@@ -0,0 +1,8 @@
+-e >seq1
+ATTA
+>seq2
+ATTA
+>seq3
+ATTA
+>seq4
+ATTA
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.figTree
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dummy.figTree Fri Feb 03 15:26:41 2017 -0500
@@ -0,0 +1,1 @@
+#NEXUS
begin taxa;
dimensions ntax=4;
taxlabels
seq1
seq2
seq3
seq4
;
end;
begin trees;
tree tree_1 = [&R] (((seq1:0.001,seq2:0.002)[&support=0.0]:0.001,seq3:0.005)[&support=0.0]:0.004,seq4:0.003)[&support=0.0]:0.001;
end;
begin figtree;
set appearance.backgroundColorAttribute="User Selection";
set appearance.backgroundColour=#-1;
set appearance.branchColorAttribute="User Selection";
set appearance.branchLineWidth=1.0;
set appearance.foregroundColour=#-16777216;
set appearance.selectionColour=#-2144520576;
set branchLabels.colorAttribute="User Selection";
set branchLabels.displayAttribute="Branch times";
set branchLabels.fontName="sansserif";
set branchLabels.fontSize=8;
set branchLabels.fontStyle=0;
set branchLabels.isShown=false;
set branchLabels.significantDigits=4;
set layout.expansion=0;
set layout.layoutType="RECTILINEAR";
set layout.zoom=0;
set nodeBars.barWidth=4.0;
set nodeLabels.colorAttribute="User Selection";
set nodeLabels.displayAttribute="support";
set nodeLabels.fontName="Arial";
set nodeLabels.fontSize=10;
set nodeLabels.fontStyle=0;
set nodeLabels.isShown=true;
set nodeLabels.significantDigits=3;
set polarLayout.alignTipLabels=false;
set polarLayout.angularRange=0;
set polarLayout.rootAngle=0;
set polarLayout.rootLength=100;
set polarLayout.showRoot=true;
set radialLayout.spread=0.0;
set rectilinearLayout.alignTipLabels=false;
set rectilinearLayout.curvature=0;
set rectilinearLayout.rootLength=100;
set scale.offsetAge=0.0;
set scale.rootAge=1.0;
set scale.scaleFactor=1.0;
set scale.scaleRoot=false;
set scaleAxis.automaticScale=true;
set scaleAxis.fontSize=8.0;
set scaleAxis.isShown=false;
set scaleAxis.lineWidth=1.0;
set scaleAxis.majorTicks=1.0;
set scaleAxis.origin=0.0;
set scaleAxis.reverseAxis=false;
set scaleAxis.showGrid=true;
set scaleAxis.significantDigits=4;
set scaleBar.automaticScale=true;
set scaleBar.fontSize=10.0;
set scaleBar.isShown=true;
set scaleBar.lineWidth=1.0;
set scaleBar.scaleRange=0.0;
set scaleBar.significantDigits=4;
set tipLabels.colorAttribute="User Selection";
set tipLabels.displayAttribute="Names";
set tipLabels.fontName="Arial";
set tipLabels.fontSize=10;
set tipLabels.fontStyle=0;
set tipLabels.isShown=true;
set tipLabels.significantDigits=4;
set trees.order=true;
set trees.orderType="increasing";
set trees.rooting=false;
set trees.rootingType="User Selection";
set trees.transform=false;
set trees.transformType="cladogram";
end;
\ No newline at end of file
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.nwk
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dummy.nwk Fri Feb 03 15:26:41 2017 -0500
@@ -0,0 +1,1 @@
+(((seq1:0.001,seq2:0.002):0.001,seq3:0.005):0.004,seq4:0.003):0.001;