updates to jaba2 from jaba release branch

[jabaws.git] / dundee-conf / settings / MafftPresets.xml

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