Merge branch 'develop' into releases/Release_2_10_0_Branch

diff --git a/examples/exampleFile.jar b/examples/exampleFile.jar
index 3231974..2f9000d 100755 (executable)
Binary files a/examples/exampleFile.jar and b/examples/exampleFile.jar differ

diff --git a/examples/exampleFile_2_3.jar b/examples/exampleFile_2_3.jar
index adf707e..1a8bef0 100644 (file)
Binary files a/examples/exampleFile_2_3.jar and b/examples/exampleFile_2_3.jar differ

diff --git a/examples/exampleFile_2_7.jar b/examples/exampleFile_2_7.jar
index 0b70e66..7cd9d77 100644 (file)
Binary files a/examples/exampleFile_2_7.jar and b/examples/exampleFile_2_7.jar differ

diff --git a/examples/ferredoxin.nw b/examples/ferredoxin.nw
index 0b949de..89ea348 100755 (executable)
--- a/examples/ferredoxin.nw
+++ b/examples/ferredoxin.nw
@@ -1 +1 @@
-(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);
+(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER1_ARATH:64.0,FER2_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);

diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa
index f314c85..80d7133 100644 (file)
--- a/examples/plantfdx.fa
+++ b/examples/plantfdx.fa
@@ -34,18 +34,18 @@ IETHKEEELTA-
 ----------------------------------------------------------ATYKVKFITPEGEQ
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
 IETHREEDMV--
->FER1_ARATH/1-148
-----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
-EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
-IETHKEEAIM--
->FER_BRANA/1-96
-----------------------------------------------------------ATYKVKFITPEGEQ
-EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
-IETHKEEELV--
 >FER2_ARATH/1-148
 ----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
 IETHKEEDIV--
+>FER_BRANA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
+IETHKEEELV--
+>FER1_ARATH/1-148
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
 >Q93Z60_ARATH/1-118
 ----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
 EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------

diff --git a/examples/uniref50.fa b/examples/uniref50.fa
index 4bdbfb4..6e6c670 100755 (executable)
--- a/examples/uniref50.fa
+++ b/examples/uniref50.fa
@@ -34,18 +34,18 @@ TIETHKEEELTA-
 -----------------------------------------------------------ATYKVKFITPEGE
 QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV
 TIETHREEDMV--
->FER1_ARATH Ferredoxin-1, chloroplast precursor
-MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
-QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
-VIETHKEEAIM--
->FER_BRANA Ferredoxin
------------------------------------------------------------ATYKVKFITPEGE
-QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
-TIETHKEEELV--
 >FER2_ARATH Ferredoxin-2, chloroplast precursor
 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
 LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
 TIETHKEEDIV--
+>FER_BRANA Ferredoxin
+-----------------------------------------------------------ATYKVKFITPEGE
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
+TIETHKEEELV--
+>FER1_ARATH Ferredoxin-1, chloroplast precursor
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
+VIETHKEEAIM--
 >Q93Z60_ARATH At1g10960/T19D16_12
 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
 QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------

diff --git a/examples/uniref50_mz.fa b/examples/uniref50_mz.fa
index 9974fc7..725d210 100644 (file)
--- a/examples/uniref50_mz.fa
+++ b/examples/uniref50_mz.fa
@@ -18,11 +18,11 @@ AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDD
 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDD
 >FER3_RAPSA/1-66 Ferredoxin, leaf L-A
 ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
->FER1_ARATH/53-118 Ferredoxin-1, chloroplast precursor
+>FER2_ARATH/53-118 Ferredoxin-1, chloroplast precursor
 ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
 >FER_BRANA/1-66 Ferredoxin
 ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDD
->FER2_ARATH/53-118 Ferredoxin-2, chloroplast precursor
+>FER1_ARATH/53-118 Ferredoxin-2, chloroplast precursor
 ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD
 >Q93Z60_ARATH/53-118 At1g10960/T19D16_12
 ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD

diff --git a/help/html/releases.html b/help/html/releases.html
index 7d34557..3fe08cb 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -63,7 +63,9 @@
           <em>General</em>
           <ul>
             <li>Colour by conservation always enabled and no tick
-                shown in menu when BLOSUM or PID shading applied</li>
+              shown in menu when BLOSUM or PID shading applied</li>
+            <li>FER1_ARATH and FER2_ARATH labels were switched in
+              example sequences/projects/trees</li>
           </ul>
           <em>Application</em>
           <ul>