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[Treebase-guts] SF.net SVN: treebase:[380] trunk/treebase-core/lib/mesquite/align
|
From: <rv...@us...> - 2009-12-15 18:37:14
|
Revision: 380
http://treebase.svn.sourceforge.net/treebase/?rev=380&view=rev
Author: rvos
Date: 2009-12-15 18:37:06 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/align/MuscleAlign/
trunk/treebase-core/lib/mesquite/align/MuscleAlign/MuscleAlign.class
trunk/treebase-core/lib/mesquite/align/Notes/
trunk/treebase-core/lib/mesquite/align/Notes/Align Notes
trunk/treebase-core/lib/mesquite/align/Notes/align.nex
trunk/treebase-core/lib/mesquite/align/Notes/bugs/
trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex
trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List
trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex
trunk/treebase-core/lib/mesquite/align/Notes/prot.nex
trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/
trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/RemoveAllGaps.class
trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/
trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.class
trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/
trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/ShiftToMinimizeStops.class
trunk/treebase-core/lib/mesquite/align/SidePusher/
trunk/treebase-core/lib/mesquite/align/SidePusher/SidePusher.class
trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab64.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab64.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft64.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight64.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover32.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover64.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/SimpleBlockMover.class
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock32.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock64.gif
trunk/treebase-core/lib/mesquite/align/ZapGaps/
trunk/treebase-core/lib/mesquite/align/ZapGaps/ZapGaps.class
trunk/treebase-core/lib/mesquite/align/ZapGapsRight/
trunk/treebase-core/lib/mesquite/align/ZapGapsRight/ZapGapsRight.class
Added: trunk/treebase-core/lib/mesquite/align/MuscleAlign/MuscleAlign.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/MuscleAlign/MuscleAlign.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/Notes/Align Notes
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/Align Notes (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/Align Notes 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,46 @@
+Align ToDo
+
+
+
+
+==============
+
+
+ - speed up getCost
+ - test code
+
+ Basic PairwiseAligner:
+ - have preprocess cost matrix for DNA data
+ - deal with terminal gaps with lower cost
+ - give it access to a user-supplied cost matrix
+ - GUI for costs
+ - preferences
+
+
+======
+Travis:
+ - pickCosts is no longer used to set the basic costs. That is now done by getDefaultCosts in AlignUtil
+
+ - I've changed the code so that it copes with amino acid data (it didn't before). e.g., alphabetLength
+ is now passed along; the substitution matrix produced by getDefaultCosts is now
+ of a size appropriate to the data
+
+ - Ambiguity codes are now dealt with. This requires different storage in the int[] A and int[]B.
+ The values in these arrays NO LONGER correspond to the A=0, C=1, G=2, T=3. Instead, the values
+ here are simply int representations of the lower 32 bits of the state set.
+ e.g., the following state sets will have the following integer values:
+ A = 1
+ C = 2
+ G = 4
+ T = 8
+ A or G = 5
+
+ This requires that when two values are compared, a method is now used to calculate the subsitution cost.
+ This function is AlignUtil.getCost(subs,a,b,alphabetLength), and it figures out the ambiguity cost.
+ We should make this faster for DNA data by having a pre-processed subs matrix that is
+ 16x16, but I just haven't managed to do that yet.
+
+ - I commented out your "score is" logging as it was taking too long!
+
+ - some of the modules I wrote (e.g., AlignMatch) now use PairwiseAligner rather than a module.
+
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/align/Notes/align.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/align.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/align.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,171 @@
+#NEXUS
+[written Tue May 02 21:58:45 MST 2006 by Mesquite version 1.06+ (build h57) at em/192.168.1.110]
+BEGIN AUTHORS;
+AUTHOR NAME = David_Maddison CODE = bembidion LASTSAVER;
+
+END;
+
+BEGIN TAXA;
+ TITLE Untitled_Taxa_Block;
+ DIMENSIONS NTAX=5;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3 taxon_4 taxon_5
+ ;
+ IDS bembidion10a77cd018680 bembidion10a77cd018681 bembidion10a77cd018682 bembidion10a77cd018683 bembidion10a77cd018684 ;
+ BLOCKID bembidion10a77cd01872;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=23;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ taxon_1 ---ACG{C,G}TT--GTTGAACCGGGG
+
+ taxon_2 ---ACGAGTTGAA----------
+
+ taxon_3 ACGTT---GTACAAC--------
+
+ taxon_4 ACGTTGGTACAAC----------
+
+ taxon_5 -----------------------
+
+
+;
+
+
+ IDS _ _ _ bembidion10a77cd33602801 bembidion10a77cd33602802 bembidion10a77cd33602803 bembidion10a77cd33602804 bembidion10a77cd33602805 bembidion10a77cd33602806 bembidion10a77cd33602807 bembidion10a77cd33602808 bembidion10a77cd33602809 bembidion10a77cd33602810 bembidion10a77cd33602811 bembidion10a77cd33602812 bembidion10a77cd33602813 bembidion10a77cd33602814 bembidion10a77cd33602815 bembidion10a77cd33602816 bembidion10a77cd33602817 bembidion10a77cd33602818 bembidion10a77cd33602819 bembidion10a77cd33602820 ;
+
+
+END;
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=7;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ taxon_1 C------
+
+ taxon_2 C------
+
+ taxon_3 -------
+
+ taxon_4 -------
+
+ taxon_5 -------
+
+
+;
+
+
+ IDS bembidion10a77d5a58420 bembidion10a77d5a58421 bembidion10a77d5a58422 bembidion10a77d5a58423 bembidion10a77d5a58424 bembidion10a77d5a58425 bembidion10a77d5a58426 ;
+
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = universal: 1 - 23;
+CODESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = universal: 1 - 7;
+
+
+END;
+
+BEGIN CHARCHANGEHISTORY;
+LINK CHARACTERS = Untitled_Character_Matrix;
+LINK CHARACTERS = Untitled_Character_Matrix;
+
+END;
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = unord: 1 - 23;
+TYPESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = unord: 1 - 7;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = 'Jukes-Cantor': 1 - 7;
+ProbModelSet * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = 'Jukes-Cantor': 1 - 7;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5103472236502170046 bembidion10a77cd01872;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 949177808083695603;
+ checksum 0 3286705137;
+ setID 1 3564779954115045874;
+ checksum 1 1310667400;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #949177808083695603 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 835 323;
+ setLocation 153 412;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ endTell;
+ setActive;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,171 @@
+#NEXUS
+[written Sat Oct 13 09:50:16 MST 2007 by Mesquite version 2.0+ (build j07) at dhcp-96875d2a.cals.arizona.edu/150.135.93.42 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=10;
+ TAXLABELS
+ Bemb_transversale_ID_2184 Bemb_transversale_NS_2158 Bemb_transversale_NS_2160 Bemb_transversale_UT_2183 Bemb_transversale_WY_2097 Bemb_transversale_ID_2164 Bemb_transversale_MT_2185 Bemb_transversale_UT_2251 Bemb_cf.transversale_CA_2321 Bemb_cf.transversale_CA_2318
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=73;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ Bemb_transversale_ID_2184 ctgaagcccgtggtcggaaacggctactgggcaatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_NS_2158 cccgtggtcggaaacggctactgggcaatgtagtgtttgggaGAGCccgtctaacccgagtactgtt------
+
+ Bemb_transversale_NS_2160 ctgaagcccgtggtcggaaAcggctactgggcaatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_UT_2183 ctgaagcccgtggtcggaaAcggctactgggcMatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_WY_2097 ctgaagcccgtggtcggaaacggctactgggcaatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_ID_2164 gcccgtctaacccgagtactgttagcgtgtccaagtccttcttgAAGGGGGCcactcg---------------
+
+ Bemb_transversale_MT_2185 gcccgtctaacccgagtactgttagcgtgtccaagtccttcttgaaGGGgGCcactcg---------------
+
+ Bemb_transversale_UT_2251 gcccgtctaacccgagtactgttagcgtgtccaagtccttcttgaaGGGGGCcactcg---------------
+
+ Bemb_cf.transversale_CA_2321 gCccgtctaacCCgagtattgttagcgtgtccaagtccttcttgAAGGGGGCcactcg---------------
+
+ Bemb_cf.transversale_CA_2318 GCccgtctaacCCgagtattgttagcGtgtccaagtcctTCTTGAAGGGGGCcactcg---------------
+
+
+;
+
+
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 73;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 73;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 73;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 1931082895948101767;
+ tell It;
+ setSelected 6 - 10;
+ setDefaultOrder 14 18 19 20 22 13 17 21 8 5;
+ attachments ;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 8552805928968270532;
+ checksum 0 3695288835 null;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #8552805928968270532 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1513 387;
+ setLocation 5 81;
+ setFont Arial;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setActive;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleShowTaxonNames on;
+ toggleTight off;
+ toggleShowChanges off;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3 2 2;
+ subCosts 10 5 10 10 10 5 5 10 10 10 5 10;
+ endTell;
+ getEmployee #mesquite.chromaseq.ColorQuality.ColorQuality;
+ tell It;
+ toggleAmbiguities on;
+ toggleMarks on;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.TextWindowMaker.TextWindowMaker;
+ tell It;
+ setText 'Pairwise aligner bug:^n^n - drop taxa 6 through 10 on 5. ^n^nNote the way the dragged sequences on the right are not aligned.';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1041 290;
+ setLocation 76 636;
+ setFont Arial;
+ setFontSize 10;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,71 @@
+clustalw option list:-
+ -help
+ -check
+ -options
+ -align
+ -newtree=filename
+ -usetree=filename
+ -newtree1=filename
+ -usetree1=filename
+ -newtree2=filename
+ -usetree2=filename
+ -bootstrap
+ -tree
+ -quicktree
+ -convert
+ -interactive
+ -batch
+ -infile=filename
+ -profile1=filename
+ -profile2=filename
+ -type=protein OR dna
+ -profile
+ -sequences
+ -matrix=filename
+ -dnamatrix=filename
+ -negative
+ -noweights
+ -gapopen=f
+ -gapext=f
+ -endgaps
+ -nopgap
+ -nohgap
+ -novgap
+ -hgapresidues=string
+ -maxdiv=n
+ -gapdist=n
+ -pwmatrix=filename
+ -pwdnamatrix=filename
+ -pwgapopen=f
+ -pwgapext=f
+ -ktuple=n
+ -window=n
+ -pairgap=n
+ -topdiags=n
+ -score=percent OR absolute
+ -transweight=f
+ -seed=n
+ -kimura
+ -tossgaps
+ -bootlabels=node OR branch
+ -debug=n
+ -output=gcg OR gde OR pir OR phylip OR nexus OR fasta
+ -outputtree=nj OR phylip OR dist OR nexus
+ -outfile=filename
+ -outorder=input OR aligned
+ -case=lower OR upper
+ -seqnos=off OR on
+ -seqno_range=off OR on
+ -range=string
+ -nosecstr1
+ -nosecstr2
+ -secstrout=structure OR mask OR both OR none
+ -helixgap=n
+ -strandgap=n
+ -loopgap=n
+ -terminalgap=n
+ -helixendin=n
+ -helixendout=n
+ -strandendin=n
+ -strandendout=n
+Peziza:~ david$
Added: trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,200 @@
+#NEXUS
+[written Sat May 06 13:12:01 MST 2006 by Mesquite version 1.06+ (build h57) at Fume-Hood-Computer.local/169.254.176.45]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=5;
+ TAXLABELS
+ Bemb_rothfelsi_NC_1951 Bemb_antiquum_MO_1963 Bemb_rothfelsi_MO_1962 Bemb_rothfelsi_MO_1961 Bemb_rothfelsi_MO_1960
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "coiPseudoRootFull.nex"';
+ DIMENSIONS NCHAR=1533;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ Bemb_rothfelsi_NC_1951 ----------------------------------------ttttggagcatgatcgggaataGtaggtActtctctaagAataCTAATTCGAGCAGAATTAGGAAACCCTGGCTCATTaatcggaGATGATCAAATTTATAATGTTATTGTAACTGCTCATGCTTTTGTAATAATTTTTTTTATAGTAATGCCAATTTTAATTGGAGGATTTGGAAATTGATTAGTTCCATTAATATTAGGAGCACCTGATATAGCCTTTCCtCGAATAAATAAtaTAAGATTCTGATTACTCCCTCCTTCATTAACTTTACTATTAATAAGTTCTATAGTAGAAAGAGGAGCTGGCACAGGTTGAACAGTGTATCCTCCACTAtcatCTTCAATTGCTCACAGAGGAGCATCCGTAGATCTAGCAATTTTTAGATTACATTTGGCAGGGGTATCTTCAATTTTAGGAGCTGTAAATTTTATTACTACAATTATTAATATACGATCTGTAGGAATAACATTTGATCGAATACCTTTATTTGTATGATCAGTAGGAATTACTGCATTATTATTACTCTTATCATTACCTGTTTTAGCTGGAGCTATTACAATATTACTAACTGATCGAAATTTAAATACTTCCTTTTTCGACCCGGCAGGAGGAGGTGATCCAATTTTATACCAACATTTATTTTGATTTTTTGGCCATCCtgaagtgtacattttgattttaccaggatttggtatAATTTCccataTTAtTaGTCaagaaAgTGGAAAAAAGGAAACATTTGGATCTTTAGGAATAATTTATGCTATATTAGCTATTGGTTTATTAGGATTTGtggtatgagCTCACCATATATTTACTGTAGGAATAGATGTTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGtgcCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAattATCTTAtagacCATCATTATTATGAGCTTTAGGATTTGTATTTTTATTTACTGTAGGAGGATTAACAGGAGTAGTTTTAGCAAATTCATCAATTGATATTGTATTACATGATACATATTATGTAGTTGCTCATTTTCATTATGTATTATCTATAGGAGCAGTATTTGCAATTATAGCTGGATTTATTCAATGATTTCCTTTGTTtacTGGATTAATAATAAACAATAATTTATTAAAAATTCAATTTATTGTTATATTTATTGGAGTAAATAtaACATTTTTTcctCAACATTTCCTAGGATTAAGAGGAatgcctcgACGATATtcagacTATCCAGATGCATATACTTCATGAAATGTAATTTCATCAATTGGATCAACAATTTCATTTATTGGAGTTTTATTATTCATTTACATTATTTGAGAAAGTTTTATTTCacaacGATTAGTTTTATtTtCtaatcAAATATCAACttctattGAATGATTACAAAaccatCcacCCgctgaacatagttactctgaactacctat--------------------------
+
+ Bemb_antiquum_MO_1963 ----------------ggatattggaactttatattttatttttggagcatgatcaggaATAGTAGGAACTTCTTTAAGAATACTAATTCGAGCAGAATTAGGAAATCCGGGCTCATTAATTGGAGACGATCAAATTTATAATGTTATTGTAACTGCTCATGCTTTTGTAATAATTTTTTTTATAGTAATACCAATTTTAATTGGAGGATTTGGAAATTGATTAGTCCCATTAATATTAGGAGCACCAGATATAGCTTTCCCACGAATAAATAATATAAGATTTTGATTACTTCCTCCTTCATTAACTTTATTATTAATAAGCTCTATGGTAGAAAGAGGGGCTGGTACAGGCTGAACAGTATACCCACCCCTATCCTCTTCAATTGCCCATAGAGGGGCATCCGTAGACCTAGCAATTTTTAGATTACATTTAGCAGGGGTATCTTCAATTTTAGGAGCTGTAAATTTTATTACTACAATTATTAATATACGATCTATAGGAATAACATTTGATCGAATACCTTTATTTGTATGATCTGTTGGAATTACTGCATTATTATTACTTTTATCTTTACCTGTCTTAGCTGGAGCTATTACAATATTATTAACTGATCGAAATTTAAATACTTCTTTTTTCGACCCGGCAGGAGGGGGTGACCCAATTTTATACCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTATATATTTTAATTTTACCTGGATTTGGTATAATTTCCCATATTATTAGCCAAGAAAGTGGAAAAAAAGAAACATTTGGATCTTTAGGAATAATTTATGCCATATTAGCTATTGGTCTATTAGGATTTGTAGTATGAGCCCACCATATGTTTACTGTAGGAATAGATGTTGATACTCGAGCTTATTTTACATCAGCTACAATAATTATTGCTGTTCCAACCGGAATTAAAATTTTTTCATGATTAGCTACATTACATGGAACACAATTATCTTATAGACCTTCATTATTATGAGCTTTAGGATTTGTATTTTTATTTACTGTAGGAGGACTAACAGGAGTAATCTTAGCAAACTCATCAATTGATATTGTATTACATGATACATATTATGTAGTTGCTCATTTTCATTATGTATTATCAATAGGAGCAGTGTTTGCAATTATAGCTGGATTTATCCAATGATTCCCGTTATTTACAGGATTAATAATAAATAATAATTTATTAAAAATTCAATTTATTATTATGTTTATTGGAGTAAATATAACATTTTTTCCTCAACATTTTTTAGGATTAAGAGGAATACCTCGACGATATTCAGACTACCCAGATGCATATACCTCATGAAATATTATTTCATCAATTGGATCAACAATTTCATTTATTGGAGTTTTATTATTTATTTATATTATTTGAGAAAGTTTTATTTCACAACGATTAATTTTATTTTCTAATCAAATACCAACTTCTATCGAATGACTACAAAATCATCCACCGGCTGAACatagttactctgaactacctata-------------------------
+
+ Bemb_rothfelsi_MO_1962 -------------------------------------------------------------------------------------------------------------cTGGCTCaTTAATTtgAgat{C,T}atcAAATTTATAATGTTATTGTaacTgctcaTGCTTTTGTAAtactTTTTtta{A,T}a{A,G}tAA{A,T}gCcaa{C,T}t{A,T}ta{A,G}ttgGagGattggGAAattgttTaGTTCc{A,C}tTAatgtaagGagc{A,C}cc{C,T}g{A,C}tATAGCctt{C,T}cctCGAATAAATAA{C,T}aTAAGattCTGATTAct{C,G}cctCCTTCATTAACTTTACTATTAATAAGTTc{C,T}{A,C}tagtaGAAAGa{G,T}gagc{C,T}ggcac{A,C}{C,G}{C,G}tTGAACAgt{A,G}taCCCTCCACTa{A,T}ga{A,C}c{C,T}tCAATTGCTCACAGAGGAGCATc{C,T}gTAGATCTAGCAATTTt{A,T}aGAT{A,T}ACATTTG{C,G}CAGGGGTat{C,G}TTCAATTTTAGGAGCTGTAAATTTTATta{C,T}taCAATTATTAATATACGATCTGTAGGAATAACATTTGATcg{A,G}aT{A,C}CC{C,T}TTATTTGTATGatc{A,T}gTAGGAATTAC{C,T}GCATTATTATT{A,G}CTCTTaTCATTACCTGTTTTAGCTGGAGCTATTACAATATta{A,T}aAaccgaTCGAAATTTAAATAct{C,T}c{C,T}tTTTTCgacCcAGCAg{A,G}agg{A,G}ggtGATCCAATTTTAta{C,T}caaCaTTTATTTTGATTTTTTGGCCATCCTGAagta{G,T}acattt{A,T}aattTtacc{A,C}gaa{A,T}ttggTATAA{A,T}TTCcc{A,C}{A,T}atta{A,T}tagtcaa{A,G}caagtggaAAAAAGGAAAC{A,C}Tt{C,T}gGATCTTt{C,G}gGAATAATt{A,T}aTGCTATATTAGCTATTGGTTTATTAGGATTTgt{A,G}gaaTgggCTCACCa{C,T}ATATTTACTGTAGga{A,C}taGAt{A,G}TTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGT{C,G}CCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAATTATCTTATACACCATCATta{A,T}taTGAGct{A,T}{A,T}agGATTTGTATTTTTATTTACTGTAGGAggacTAACAGGAGTAGTTTTAGCAAATTCATCAATTGATAT{A,T}GTATTACACGATACAtGTTATGTAGTTG{C,G}TCATTTTCATTATGTATTATCTATAGGAGC{A,C}GTATt{G,T}gCAa{C,T}taaAGCTGGATTTATTCAATGATt{C,T}cCTTTATTTGCTGG{A,G}TTAATAATAAACAA{A,T}AATTTATTAAAAA{C,T}TCAATTt{A,T}tTGTTATATTTATt{G,T}gagTAAATATGACATTTTTt{C,T}{C,T}t{C,T}aACATTTCCTAGGATTAag{A,G}gGAATTcct{C,T}gacgatATtta{A,G}actatccAgATGCATATACTTCATGAAATGTAATTTcaTCAattgGATCAACAATTt{C,T}attTATtggag{G,T}tTta{A,T}tattta{A,T}tTATattattTgagaaagttttatttcaa{A,G}acgattagttttaattt{C,T}t{A,T}a{C,T}caaat--------------------------------------------------------------------------------------------
+
+ Bemb_rothfelsi_MO_1961 ------------------------------------------------------------------------------------------------------------CctggctcaTTAAtttgAgat{C,T}atcAAATTTATAatgttATtgtaacTGCTCATGCTTTtgtaata{A,C}tttTTtta{A,T}a{A,G}tAa{A,T}gccaa{A,C}tt{C,T}{A,T}{A,G}tt{G,T}Ga{A,G}g{A,G}ttgggaaa{A,T}t{G,T}{G,T}ttag{C,T}Tcc{A,C}ttaa{A,T}g{G,T}aa{A,G}{G,T}agcacc{C,T}g{A,C}{C,T}aT{A,T}GCctttc{C,G}{G,T}cGAa{G,T}aAAtaa{C,T}ataag{A,T}tt{C,T}tGATTAct{C,G}c{C,G}{G,T}cc{G,T}TCATTA{A,G}{C,G}TTTACtatTAA{A,T}AA{G,T}Tt{C,T}{C,T}atagtagAAaga{G,T}gagc{C,T}g{C,G}cac{A,C}{C,G}{C,G}{C,T}TGAACAgt{A,G}t{A,G}CCCTCCa{C,T}T{A,C}t{C,G}a{C,T}c{C,T}tCAATTGCTCACAGAGgagc{A,T}t{C,T}{C,T}gtAGATCTAGCAA{G,T}TTt{A,T}aGATTACATTTG{C,G}CAGGGGTat{C,G}TTCAATTTTAGGAGCT{C,G}TAAATTTTATTa{A,C}taC{A,C}ATTATTAATATACGATCTGTAGGAATAACATT{G,T}GATcg{A,G}aTACCTT{C,T}ATTTGTA{C,T}GATCAGTAGGAA{A,T}TAC{C,T}GC{A,C}TtaTTATTACTCTTATCATTACCTGTTTTAGCTGGAGCTATTACAATATTa{A,T}aAaccgatCGAAA{C,T}TTAAATACtTcctttTTCGAcCcAGCAggaggaggtGATCCAATTTTAta{C,T}caacatttATTTTGATTTTTTGGCCATCCTGAAgtatac{A,C}ttttaattTtaccag{A,G}{A,G}tttgg{G,T}a{A,T}aA{A,T}TTCcc{A,C}tatta{A,T}ta{A,G}tcaagcaag{G,T}ggaAAAAaggaAACatt{C,T}ggaTCTTt{C,T}ggAATAATt{A,T}aTGCTATATTAGCTATTGGTTTATTAGGATTTgtagaaTg{A,G}gCTCACCa{C,T}ATATTTACTGTAGg{A,G}{A,C}taGAt{A,G}tTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGt{C,G}CCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAA{C,T}TATCTTATACACCATCATta{A,T}{A,T}aTGAGct{A,T}{A,T}agGATTTGTATTTTTATTTACTGTAGGAGGA{C,T}TAACAGGAGTAGTTTTAGCAAATTCATCAATTGATATTGTATTACACGATACAtGTTATGTAGTTGCTCATTTTCATTATGTATTATCTaTAGGAGCAGTatt{G,T}gcaa{C,T}ta{A,T}aG{C,G}TGGATTTATTCAATGatt{C,T}{C,T}ctTTATTTG{C,G}TGGATTAATAATAAACAATAATTTATTAAAAA{C,T}tcaAttt{A,T}ttgTTATATTTatt{G,T}gagTAAATATGACATTTTTt{C,T}{C,T}tcAACATTTCCTAGGATTAAG{A,G}GGAATTcct{C,T}gacgAtATtta{A,G}actatccAgATGCATATACTTCATGAAATGTAATTTCATcaattgGATCAAcAATTt{C,T}atttattggagttTTattatt{C,T}attTATattatttgagaaagttttatttca{A,C}{A,G}acgattagttttaattt{C,T}taa{C,T}caaat--------------------------------------------------------------------------------------------
+
+ Bemb_rothfelsi_MO_1960 -------------------------------------------------------------------------------------------------------------CTggctcaTTAAtTtGAgat{C,T}atcAAATTTAtAatgttattgtaacTGCTCATGCTTTTGTAAtactTTTTtta{A,T}a{A,G}taa{A,T}g{C,G}c{A,C}a{A,C}tt{C,T}a{A,G}ttgga{A,G}ga{A,T}tggGAAattg{G,T}tta{A,G}tt{C,T}c{A,C}ttaa{A,T}g{G,T}aa{A,G}g{A,G}{A,G}c{A,C}cc{C,T}ga{A,T}a{A,T}{A,T}gcc{C,T}t{C,T}cc{C,T}c{C,G}aataaaTaac{A,C}taa{A,G}{A,G}{A,T}t{C,T}{C,T}ga{A,T}tac{C,T}tcc{C,T}cc{C,T}tc{A,C}ttaactttac{C,T}a{A,T}taa{A,T}aa{A,G}ttc{C,T}atggaa{A,G}aaa{A,G}a{A,T}ga{A,G}c{C,T}gg{C,G}{A,C}c{C,G}{A,G}gttgaa{A,C}a{A,G}tatAccc{C,T}cca{A,C}ta{A,T}ga{A,C}c{C,T}t{C,T}aattg{C,G}{C,T}ca{A,C}a{A,G}a{A,G}ga{A,G}c{A,C}t{C,T}{C,T}g{G,T}a{A,G}a{A,T}{C,T}{C,T}agc{A,C}aTttt{A,T}a{A,G}a{A,T}ta{A,C}{A,C}tttgg{C,G}a{A,G}ggg{G,T}{A,T}tatt{C,T}{A,C}{A,T}tttta{A,G}{A,G}a{A,G}c{C,T}g{G,T}aAATTTTATtattac{A,C}attATTAAta{A,T}acGATC{C,T}G{G,T}aGGAATAA{A,C}{A,C}tttgatc{C,G}ga{A,T}acc{C,T}ttaTTTg{G,T}A{C,T}G{A,G}{A,T}ttg{G,T}aggaattac{C,T}gc{A,C}{G,T}tattatt{A,G}ctc{A,T}{C,T}atc{A,C}{C,T}{C,T}{A,G}CCT{C,G}TTTTAGCTG{C,G}AGc{A,T}ATTAcaat{A,T}Tta{A,T}aaaccgatCGAAATTTAAATACttc{C,G}tt{A,T}ttcGACCCagcag{A,G}agg{A,G}ggTGATCCAATTTTAta{C,T}caacatTTATT{G,T}TGATTTTTTGGCCATCC{C,T}Gaa{C,G}tatacattt{A,T}aattTtaccaga{A,G}tttggtataa{A,T}ttccc{A,C}tatta{A,T}tagtc{A,C}agcaag{G,T}gg{A,G}AAAAAGgAAACatt{C,T}ggaTCttt{A,C}ggaATAATTAATGCTATATTAGCTATTGGTTTATTAGGATTTgtagaaTgggCTCACCa{C,T}ATATTTACTGTAGga{A,C}tagAt{A,G}TTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGT{C,G}CCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAATTATCTTATACACCATCATta{A,T}taTGAGct{A,T}{A,T}agGATTTGTATTTTTATTTACTGTAGGAGGACTAACAGGAGTAGTTTTAGCAAATTCATCAATTGATATTGTATTAc{A,C}cGATACAtGTTATGTAGTTGCTCATTTTCATTATGTATTATCTaTAGGAGCAGTATt{G,T}gCAa{C,T}taaaGCTGGATTTATTCAATGattccctTTATTTG{C,G}TGG{A,G}TTAATAAT{A,T}AAC{A,C}A{A,T}AATTTATTAAAAA{C,T}tCAAttt{A,T}ttgTTATATTTatt{G,T}gagTAAATATGACATTTTTt{C,T}{C,T}tcAACATTTCCTAGGATTAAG{A,G}GGAATTcct{C,T}gacGATATtta{A,G}actATCCAGATGCATATACTTCATGAAATGTAATTTCATCAattgGATCAACAATtt{C,T}atttattgg{A,G}g{G,T}tTTa{A,T}tatttattTATattattTgagaaagtttTAtttca{A,C}{A,G}acgattagttttaattt{C,T}taa{C,T}caatatc{A,C}actttcatcg{A,C}atgattacaaaatcatccacccgctga---------------------------------------------------
+
+
+;
+
+
+
+END;
+
+BEGIN CODONS;
+CODONPOSSET * UNTITLED = 1: 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 159 162 165 168 171 174 177 180 183 186 189 192 195 198 201 204 207 210 213 216 219 222 225 228 231 234 237 240 243 246 249 252 255 258 261 264 267 270 273 276 279 282 285 288 291 294 297 300 303 306 309 312 315 318 321 324 327 330 333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 381 384 387 390 393 396 399 402 405 408 411 414 417 420 423 426 429 432 435 438 441 444 447 450 453 456 459 462 465 468 471 474 477 480 483 486 489 492 495 498 501 504 507 510 513 516 519 522 525 528 531 534 537 540 543 546 549 552 555 558 561 564 567 570 573 576 579 582 585 588 591 594 597 600 603 606 609 612 615 618 621 624 627 630 633 636 639 642 645 648 651 654 657 660 663 666 669 672 675 678 681 684 687 690 693 696 699 702 705 708 711 714 717 720 723 726 729 732 735 738 741 744 747 750 753 756 759 762 765 768 771 774 777 780 783 786 789 792 795 798 801 804 807 810 813 816 819 822 825 828 831 834 837 840 843 846 849 852 855 858 861 864 867 870 873 876 879 882 885 888 891 894 897 900 903 906 909 912 915 918 921 924 927 930 933 936 939 942 945 948 951 954 957 960 963 966 969 972 975 978 981 984 987 990 993 996 999 1002 1005 1008 1011 1014 1017 1020 1023 1026 1029 1032 1035 1038 1041 1044 1047 1050 1053 1056 1059 1062 1065 1068 1071 1074 1077 1080 1083 1086 1089 1092 1095 1098 1101 1104 1107 1110 1113 1116 1119 1122 1125 1128 1131 1134 1137 1140 1143 1146 1149 1152 1155 1158 1161 1164 1167 1170 1173 1176 1179 1182 1185 1188 1191 1194 1197 1200 1203 1206 1209 1212 1215 1218 1221 1224 1227 1230 1233 1236 1239 1242 1245 1248 1251 1254 1257 1260 1263 1266 1269 1272 1275 1278 1281 1284 1287 1290 1293 1296 1299 1302 1305 1308 1311 1314 1317 1320 1323 1326 1329 1332 1335 1338 1341 1344 1347 1350 1353 1356 1359 1362 1365 1368 1371 1374 1377 1380 1383 1386 1389 1392 1395 1398 1401 1404 1407 1410 1413 1416 1419 1422 1425 1428 1431 1434 1437 1440 1443 1446 1449 1452 1455 1458 1461 1464 1467 1470 1473 1476 1479 1482 1485 1488 1491 1494 1497 1500 1503 1506 1509 1512 1515 1518 1521 1524 1527 1530 1533, 2: 1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94 97 100 103 106 109 112 115 118 121 124 127 130 133 136 139 142 145 148 151 154 157 160 163 166 169 172 175 178 181 184 187 190 193 196 199 202 205 208 211 214 217 220 223 226 229 232 235 238 241 244 247 250 253 256 259 262 265 268 271 274 277 280 283 286 289 292 295 298 301 304 307 310 313 316 319 322 325 328 331 334 337 340 343 346 349 352 355 358 361 364 367 370 373 376 379 382 385 388 391 394 397 400 403 406 409 412 415 418 421 424 427 430 433 436 439 442 445 448 451 454 457 460 463 466 469 472 475 478 481 484 487 490 493 496 499 502 505 508 511 514 517 520 523 526 529 532 535 538 541 544 547 550 553 556 559 562 565 568 571 574 577 580 583 586 589 592 595 598 601 604 607 610 613 616 619 622 625 628 631 634 637 640 643 646 649 652 655 658 661 664 667 670 673 676 679 682 685 688 691 694 697 700 703 706 709 712 715 718 721 724 727 730 733 736 739 742 745 748 751 754 757 760 763 766 769 772 775 778 781 784 787 790 793 796 799 802 805 808 811 814 817 820 823 826 829 832 835 838 841 844 847 850 853 856 859 862 865 868 871 874 877 880 883 886 889 892 895 898 901 904 907 910 913 916 919 922 925 928 931 934 937 940 943 946 949 952 955 958 961 964 967 970 973 976 979 982 985 988 991 994 997 1000 1003 1006 1009 1012 1015 1018 1021 1024 1027 1030 1033 1036 1039 1042 1045 1048 1051 1054 1057 1060 1063 1066 1069 1072 1075 1078 1081 1084 1087 1090 1093 1096 1099 1102 1105 1108 1111 1114 1117 1120 1123 1126 1129 1132 1135 1138 1141 1144 1147 1150 1153 1156 1159 1162 1165 1168 1171 1174 1177 1180 1183 1186 1189 1192 1195 1198 1201 1204 1207 1210 1213 1216 1219 1222 1225 1228 1231 1234 1237 1240 1243 1246 1249 1252 1255 1258 1261 1264 1267 1270 1273 1276 1279 1282 1285 1288 1291 1294 1297 1300 1303 1306 1309 1312 1315 1318 1321 1324 1327 1330 1333 1336 1339 1342 1345 1348 1351 1354 1357 1360 1363 1366 1369 1372 1375 1378 1381 1384 1387 1390 1393 1396 1399 1402 1405 1408 1411 1414 1417 1420 1423 1426 1429 1432 1435 1438 1441 1444 1447 1450 1453 1456 1459 1462 1465 1468 1471 1474 1477 1480 1483 1486 1489 1492 1495 1498 1501 1504 1507 1510 1513 1516 1519 1522 1525 1528 1531, 3: 2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47 50 53 56 59 62 65 68 71 74 77 80 83 86 89 92 95 98 101 104 107 110 113 116 119 122 125 128 131 134 137 140 143 146 149 152 155 158 161 164 167 170 173 176 179 182 185 188 191 194 197 200 203 206 209 212 215 218 221 224 227 230 233 236 239 242 245 248 251 254 257 260 263 266 269 272 275 278 281 284 287 290 293 296 299 302 305 308 311 314 317 320 323 326 329 332 335 338 341 344 347 350 353 356 359 362 365 368 371 374 377 380 383 386 389 392 395 398 401 404 407 410 413 416 419 422 425 428 431 434 437 440 443 446 449 452 455 458 461 464 467 470 473 476 479 482 485 488 491 494 497 500 503 506 509 512 515 518 521 524 527 530 533 536 539 542 545 548 551 554 557 560 563 566 569 572 575 578 581 584 587 590 593 596 599 602 605 608 611 614 617 620 623 626 629 632 635 638 641 644 647 650 653 656 659 662 665 668 671 674 677 680 683 686 689 692 695 698 701 704 707 710 713 716 719 722 725 728 731 734 737 740 743 746 749 752 755 758 761 764 767 770 773 776 779 782 785 788 791 794 797 800 803 806 809 812 815 818 821 824 827 830 833 836 839 842 845 848 851 854 857 860 863 866 869 872 875 878 881 884 887 890 893 896 899 902 905 908 911 914 917 920 923 926 929 932 935 938 941 944 947 950 953 956 959 962 965 968 971 974 977 980 983 986 989 992 995 998 1001 1004 1007 1010 1013 1016 1019 1022 1025 1028 1031 1034 1037 1040 1043 1046 1049 1052 1055 1058 1061 1064 1067 1070 1073 1076 1079 1082 1085 1088 1091 1094 1097 1100 1103 1106 1109 1112 1115 1118 1121 1124 1127 1130 1133 1136 1139 1142 1145 1148 1151 1154 1157 1160 1163 1166 1169 1172 1175 1178 1181 1184 1187 1190 1193 1196 1199 1202 1205 1208 1211 1214 1217 1220 1223 1226 1229 1232 1235 1238 1241 1244 1247 1250 1253 1256 1259 1262 1265 1268 1271 1274 1277 1280 1283 1286 1289 1292 1295 1298 1301 1304 1307 1310 1313 1316 1319 1322 1325 1328 1331 1334 1337 1340 1343 1346 1349 1352 1355 1358 1361 1364 1367 1370 1373 1376 1379 1382 1385 1388 1391 1394 1397 1400 1403 1406 1409 1412 1415 1418 1421 1424 1427 1430 1433 1436 1439 1442 1445 1448 1451 1454 1457 1460 1463 1466 1469 1472 1475 1478 1481 1484 1487 1490 1493 1496 1499 1502 1505 1508 1511 1514 1517 1520 1523 1526 1529 1532;
+CODONPOSSET CodonPositions = 1: 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 159 162 165 168 171 174 177 180 183 186 189 192 195 198 201 204 207 210 213 216 219 222 225 228 231 234 237 240 243 246 249 252 255 258 261 264 267 270 273 276 279 282 285 288 291 294 297 300 303 306 309 312 315 318 321 324 327 330 333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 381 384 387 390 393 396 399 402 405 408 411 414 417 420 423 426 429 432 435 438 441 444 447 450 453 456 459 462 465 468 471 474 477 480 483 486 489 492 495 498 501 504 507 510 513 516 519 522 525 528 531 534 537 540 543 546 549 552 555 558 561 564 567 570 573 576 579 582 585 588 591 594 597 600 603 606 609 612 615 618 621 624 627 630 633 636 639 642 645 648 651 654 657 660 663 666 669 672 675 678 681 684 687 690 693 696 699 702 705 708 711 714 717 720 723 726 729 732 735 738 741 744 747 750 753 756 759 762 765 768 771 774 777 780 783 786 789 792 795 798 801 804 807 810 813 816 819 822 825 828 831 834 837 840 843 846 849 852 855 858 861 864 867 870 873 876 879 882 885 888 891 894 897 900 903 906 909 912 915 918 921 924 927 930 933 936 939 942 945 948 951 954 957 960 963 966 969 972 975 978 981 984 987 990 993 996 999 1002 1005 1008 1011 1014 1017 1020 1023 1026 1029 1032 1035 1038 1041 1044 1047 1050 1053 1056 1059 1062 1065 1068 1071 1074 1077 1080 1083 1086 1089 1092 1095 1098 1101 1104 1107 1110 1113 1116 1119 1122 1125 1128 1131 1134 1137 1140 1143 1146 1149 1152 1155 1158 1161 1164 1167 1170 1173 1176 1179 1182 1185 1188 1191 1194 1197 1200 1203 1206 1209 1212 1215 1218 1221 1224 1227 1230 1233 1236 1239 1242 1245 1248 1251 1254 1257 1260 1263 1266 1269 1272 1275 1278 1281 1284 1287 1290 1293 1296 1299 1302 1305 1308 1311 1314 1317 1320 1323 1326 1329 1332 1335 1338 1341 1344 1347 1350 1353 1356 1359 1362 1365 1368 1371 1374 1377 1380 1383 1386 1389 1392 1395 1398 1401 1404 1407 1410 1413 1416 1419 1422 1425 1428 1431 1434 1437 1440 1443 1446 1449 1452 1455 1458 1461 1464 1467 1470 1473 1476 1479 1482 1485 1488 1491 1494 1497 1500 1503 1506 1509 1512 1515 1518 1521 1524 1527 1530 1533, 2: 1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94 97 100 103 106 109 112 115 118 121 124 127 130 133 136 139 142 145 148 151 154 157 160 163 166 169 172 175 178 181 184 187 190 193 196 199 202 205 208 211 214 217 220 223 226 229 232 235 238 241 244 247 250 253 256 259 262 265 268 271 274 277 280 283 286 289 292 295 298 301 304 307 310 313 316 319 322 325 328 331 334 337 340 343 346 349 352 355 358 361 364 367 370 373 376 379 382 385 388 391 394 397 400 403 406 409 412 415 418 421 424 427 430 433 436 439 442 445 448 451 454 457 460 463 466 469 472 475 478 481 484 487 490 493 496 499 502 505 508 511 514 517 520 523 526 529 532 535 538 541 544 547 550 553 556 559 562 565 568 571 574 577 580 583 586 589 592 595 598 601 604 607 610 613 616 619 622 625 628 631 634 637 640 643 646 649 652 655 658 661 664 667 670 673 676 679 682 685 688 691 694 697 700 703 706 709 712 715 718 721 724 727 730 733 736 739 742 745 748 751 754 757 760 763 766 769 772 775 778 781 784 787 790 793 796 799 802 805 808 811 814 817 820 823 826 829 832 835 838 841 844 847 850 853 856 859 862 865 868 871 874 877 880 883 886 889 892 895 898 901 904 907 910 913 916 919 922 925 928 931 934 937 940 943 946 949 952 955 958 961 964 967 970 973 976 979 982 985 988 991 994 997 1000 1003 1006 1009 1012 1015 1018 1021 1024 1027 1030 1033 1036 1039 1042 1045 1048 1051 1054 1057 1060 1063 1066 1069 1072 1075 1078 1081 1084 1087 1090 1093 1096 1099 1102 1105 1108 1111 1114 1117 1120 1123 1126 1129 1132 1135 1138 1141 1144 1147 1150 1153 1156 1159 1162 1165 1168 1171 1174 1177 1180 1183 1186 1189 1192 1195 1198 1201 1204 1207 1210 1213 1216 1219 1222 1225 1228 1231 1234 1237 1240 1243 1246 1249 1252 1255 1258 1261 1264 1267 1270 1273 1276 1279 1282 1285 1288 1291 1294 1297 1300 1303 1306 1309 1312 1315 1318 1321 1324 1327 1330 1333 1336 1339 1342 1345 1348 1351 1354 1357 1360 1363 1366 1369 1372 1375 1378 1381 1384 1387 1390 1393 1396 1399 1402 1405 1408 1411 1414 1417 1420 1423 1426 1429 1432 1435 1438 1441 1444 1447 1450 1453 1456 1459 1462 1465 1468 1471 1474 1477 1480 1483 1486 1489 1492 1495 1498 1501 1504 1507 1510 1513 1516 1519 1522 1525 1528 1531, 3: 2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47 50 53 56 59 62 65 68 71 74 77 80 83 86 89 92 95 98 101 104 107 110 113 116 119 122 125 128 131 134 137 140 143 146 149 152 155 158 161 164 167 170 173 176 179 182 185 188 191 194 197 200 203 206 209 212 215 218 221 224 227 230 233 236 239 242 245 248 251 254 257 260 263 266 269 272 275 278 281 284 287 290 293 296 299 302 305 308 311 314 317 320 323 326 329 332 335 338 341 344 347 350 353 356 359 362 365 368 371 374 377 380 383 386 389 392 395 398 401 404 407 410 413 416 419 422 425 428 431 434 437 440 443 446 449 452 455 458 461 464 467 470 473 476 479 482 485 488 491 494 497 500 503 506 509 512 515 518 521 524 527 530 533 536 539 542 545 548 551 554 557 560 563 566 569 572 575 578 581 584 587 590 593 596 599 602 605 608 611 614 617 620 623 626 629 632 635 638 641 644 647 650 653 656 659 662 665 668 671 674 677 680 683 686 689 692 695 698 701 704 707 710 713 716 719 722 725 728 731 734 737 740 743 746 749 752 755 758 761 764 767 770 773 776 779 782 785 788 791 794 797 800 803 806 809 812 815 818 821 824 827 830 833 836 839 842 845 848 851 854 857 860 863 866 869 872 875 878 881 884 887 890 893 896 899 902 905 908 911 914 917 920 923 926 929 932 935 938 941 944 947 950 953 956 959 962 965 968 971 974 977 980 983 986 989 992 995 998 1001 1004 1007 1010 1013 1016 1019 1022 1025 1028 1031 1034 1037 1040 1043 1046 1049 1052 1055 1058 1061 1064 1067 1070 1073 1076 1079 1082 1085 1088 1091 1094 1097 1100 1103 1106 1109 1112 1115 1118 1121 1124 1127 1130 1133 1136 1139 1142 1145 1148 1151 1154 1157 1160 1163 1166 1169 1172 1175 1178 1181 1184 1187 1190 1193 1196 1199 1202 1205 1208 1211 1214 1217 1220 1223 1226 1229 1232 1235 1238 1241 1244 1247 1250 1253 1256 1259 1262 1265 1268 1271 1274 1277 1280 1283 1286 1289 1292 1295 1298 1301 1304 1307 1310 1313 1316 1319 1322 1325 1328 1331 1334 1337 1340 1343 1346 1349 1352 1355 1358 1361 1364 1367 1370 1373 1376 1379 1382 1385 1388 1391 1394 1397 1400 1403 1406 1409 1412 1415 1418 1421 1424 1427 1430 1433 1436 1439 1442 1445 1448 1451 1454 1457 1460 1463 1466 1469 1472 1475 1478 1481 1484 1487 1490 1493 1496 1499 1502 1505 1508 1511 1514 1517 1520 1523 1526 1529 1532;
+
+CODESET * UNTITLED = universal: 1 - 1533;
+
+
+END;
+
+BEGIN paup;
+ outgroup Bemb_californicum_CA_1451 Bemb_concolor_NS_1470;
+
+END;
+BEGIN ASSUMPTIONS;
+ OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 1533;
+
+ EXSET * UNTITLED = 1 - 50 1479 - 1533;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1533;
+END;
+
+BEGIN MacClade;
+ Version 4.0 87;
+ LastModified -1071261665;
+ FileSettings editor '0' '0' '1' '1';
+ Singles 000;
+ Editor 00011001110111100100010111 '4' '8' Geneva '9' '216' '1' all;
+ EditorPosition '70' '118' '643' '999';
+ TreeWindowPosition '46' '6' '809' '1230';
+ ListWindow Characters closed Geneva '9' '70' '45' '129' '406' 000;
+ ListWindow Taxa closed Geneva '9' '50' '10' '276' '490' 100000000;
+ ListWindow Trees closed Geneva '9' '50' '10' '276' '490';
+ ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow WtSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow ExSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow CharSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490';
+ ListWindow CharPartNames closed Geneva '9' '50' '10' '276' '490';
+ ListWindow WtSets closed Geneva '9' '50' '10' '276' '490';
+ ChartWindowPosition '52' '30' '772' '1220';
+ StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220';
+ WindowOrder Data;
+ OtherSymbols & / 00 ? -;
+ Correlation '0' '0' '1000' '0' '0' 10011010;
+ Salmo 00000001;
+ EditorFile '4';
+ ExportHTML _ MOSS '100' 110000;
+ PrettyPrint 10;
+ EditorToolsPosition '720' '44' '115' '165';
+ TreeWindowProgram 10;
+ TreeWindow 0000;
+ Continuous '0' '3' 1;
+ Calculations 0000001;
+ SummaryMode '0' '0' 0;
+ Charts Geneva '9' ( normal ) 0010;
+ NexusOptions '0' '0' '50' 001011011;
+ TipLabel '1';
+ TreeFont Geneva '9' ( normal );
+ TreeShape 1.0 1.0 0100;
+ TraceLabels 0101;
+ ChartColors '0' '0' '65535' '9' '0' 1;
+ ChartBiggestSpot 1;
+ ChartPercent 10;
+ ChartBarWidth '10' 1;
+ ChartVerticalAxis 10101;
+ ChartMinMax '0';
+ TraceAllChangesDisplay '1' 1;
+ BarsOnBranchesDisplay '0' '0' '60000' '10000' '10000' '10000' '10000' '60000' '65000' '65000' '65000' '6' '1' 0000101;
+ ContinuousBranchLabels 0;
+ AllStatesBranchLabels 1;
+ IndexNotation '2' 1;
+ PrintTree 10.00 '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' Geneva '9' ( normal ) Geneva '10' ( normal ) Geneva '9' ( normal ) Geneva '9' ( normal ) Geneva '9' ( bold ) Geneva '9' ( normal ) Geneva '9' ( normal ) '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '0' '0' '-39' '4' '-40' '0' '1' '2' '1' '8' '0' '0' '0' '2' 1000111000000000000100000111000;
+ MatchChar 00 .;
+ EntryInterpretation 01;
+ ColorOptions 00;
+ TreeTools '0' '5' '4' '0' '10' '4' '0' 00100111111101110;
+ EditorTools '0' '0' '0' '1000' '0' '0' '6' '3' '0' 100010101110001;
+ PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010;
+ BothTools '1';
+
+END;
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6370606309008394174;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 6733066121074379816;
+ checksum 0 2978122628;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #6733066121074379816 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 1484 556;
+ setLocation 60 22;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ endTell;
+ setActive;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges off;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/Notes/prot.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/prot.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/prot.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,153 @@
+#NEXUS
+[written Sun Apr 30 12:16:37 MST 2006 by Mesquite version 1.06+ (build h57) at david-maddisons-computer.local/192.168.0.4]
+
+BEGIN TAXA;
+ TITLE Untitled_Taxa_Block;
+ DIMENSIONS NTAX=3;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=15;
+ FORMAT DATATYPE = Protein GAP = - MISSING = ?;
+ MATRIX
+ taxon_1 AGVLTT--GGVL---
+
+ taxon_2 HGEQPGVLTTGGMNI
+
+ taxon_3 MFGATACCTCEQRDM
+
+
+;
+
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 15;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 15;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 15;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5649887706477911529;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 5596208106298272285;
+ checksum 0 3074286207;
+ endTell;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ showTaxa #5649887706477911529 #mesquite.lists.TaxonList.TaxonList;
+ tell It;
+ setTaxa #5649887706477911529;
+ getWindow;
+ tell It;
+ newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder;
+ newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
+ setSize 360 400;
+ setLocation 60 22;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #5596208106298272285 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 699 286;
+ setLocation 113 176;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ endTell;
+ setActive;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWithCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/RemoveAllGaps.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/RemoveAllGaps.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/ShiftToMinimizeStops.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/ShiftToMinimizeStops.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/SidePusher.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/SidePusher.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab32.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab64.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab32.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab64.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft32.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft64.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight32.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight64.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover.gif
===================================================================
(Binary files differ)
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover32.gif
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover64.gif
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Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover64.gif
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/SimpleBlockMover.class
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Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/SimpleBlockMover.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock.gif
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Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock.gif
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock32.gif
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Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock32.gif
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock64.gif
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Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock64.gif
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ZapGaps/ZapGaps.class
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Property cha...
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