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diff --git a/dundee-conf/settings/MafftPresets.xml b/dundee-conf/settings/MafftPresets.xml
deleted file mode 100644
index 794d20c..0000000
--- a/dundee-conf/settings/MafftPresets.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
-<presets>
-	<runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>
-	<preset>
-		<name>L-INS-i (Accuracy-oriented)</name>
-		<description>L-INS-i (probably most accurate; recommended for &lt;200
-			sequences; iterative refinement method incorporating local pairwise
-			alignment information)</description>
-		<optlist>
-			<option>--localpair</option>
-			<option>--maxiterate 1000</option>
-		</optlist>
-	</preset>
-	<preset>
-		<name>G-INS-i (Accuracy-oriented)</name>
-		<description>G-INS-i (suitable for sequences of similar lengths;
-			recommended for &lt;200 sequences; iterative refinement method
-			incorporating global pairwise alignment information)</description>
-		<optlist>
-			<option>--globalpair</option>
-			<option>--maxiterate 1000</option>
-		</optlist>
-	</preset>
-	<preset>
-		<name>E-INS-i (Accuracy-oriented)</name>
-		<description>E-INS-i (suitable for sequences containing large
-			unalignable regions; recommended for &lt;200 sequences)</description>
-		<optlist>
-			<option>--ep 0</option>
-			<option>--genafpair</option>
-			<option>--maxiterate 1000</option>
-		</optlist>
-	</preset>
-	<preset>
-		<name>FFT-NS-i (Speed oriented)</name>
-		<description>FFT-NS-i (iterative refinement method; two cycles only)</description>
-		<optlist>
-			<option>--retree 2</option>
-			<option>--maxiterate 2</option>
-		</optlist>
-	</preset>
-	<preset>
-		<name>FFT-NS-1 (Speed oriented)</name>
-		<description>FFT-NS-1 (very fast; recommended for &gt;2000 sequences;
-			progressive method with a rough guide tree)</description>
-		<optlist>
-			<option>--retree 1</option>
-			<option>--maxiterate 0</option>
-		</optlist>
-	</preset>
-	<preset>
-		<name>NW-NS-PartTree-1 (Speed oriented)</name>
-		<description>NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000
-			sequences; progressive method with the PartTree algorithm)</description>
-		<optlist>
-			<option>--retree 1</option>
-			<option>--maxiterate 0</option>
-			<option>--nofft</option>
-			<option>--parttree</option>
-		</optlist>
-	</preset>
-</presets>