From: amwaterhouse Date: Thu, 2 Jun 2005 12:28:08 +0000 (+0000) Subject: new X-Git-Tag: Release_2_0~118 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c48c20802e5bc8dd4ff241bf9947a8ad94f20669;p=jalview.git new --- diff --git a/website/Templates/jtemplate.dwt b/website/Templates/jtemplate.dwt new file mode 100755 index 0000000..69b84d6 --- /dev/null +++ b/website/Templates/jtemplate.dwt @@ -0,0 +1,67 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

Contents +
+
+ + diff --git a/website/version2/examples/applets.html b/website/version2/examples/applets.html new file mode 100755 index 0000000..b811a99 --- /dev/null +++ b/website/version2/examples/applets.html @@ -0,0 +1,145 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+

Jalview2 comes in two distinct flavours.
+
+ The main application allows connection to multiple web services provided + at the University of Dundee as well as a host of additional useful features + such as printing, making images from your alignment and annotating your + alignment.
+ You need to download and install this software.

+

Pressing one of the buttons below will load up a cut down version + of Jalview2 multiple alignment editor, which runs within your web browser.

+

Alignment 1 - Serine proteases (6 sequences x 279 residues)

+
+ + + + + +
+

Alignment 2 - Lipases (16 sequences x 487 residues)

+
+ + + + +
+

Alignment 3 - Glutathione S-transferases (61 sequences x 290 residues) With associated tree

+
+ + + + + + + +
+

The applet takes the following Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
namevalue
filefileName
showFullIdtrue false
showAnnotationtrue false
showConservationtrue false
showQualitytrue false
showConsensustrue false
defaultColourClustal, Blosum62, % Identity, Zappo, Hydrophobic, Helix Propensity, + Strand Propensity, Turn Propensity, Buried Index, Nucleotide
+

 

+ +
+
+ + diff --git a/website/version2/examples/examples.html b/website/version2/examples/examples.html new file mode 100755 index 0000000..59194f5 --- /dev/null +++ b/website/version2/examples/examples.html @@ -0,0 +1,83 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+

Many alignment tools which require time consuming and/or large proccessing + power are currently being developed as Web Services within the Barton + Group, Dundee, and added to the Jalview interface.

+

 

+
+ + + + +
+
+

 

+

 

+

Next + >

+ +
+
+ + diff --git a/website/version2/examples/examples2.html b/website/version2/examples/examples2.html new file mode 100755 index 0000000..f453b83 --- /dev/null +++ b/website/version2/examples/examples2.html @@ -0,0 +1,78 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+

Several of the most popular sequence alignment algorithms and / or + programs have been implemented as web services which Jalview has access + to.

+

The figure below shows the web service status window indicating that + a Muscle Alignment job as run to completion. The window shows important + feedback regarding the alignement.

+

+

 

+

< + Back    Next >

+ +
+
+ + diff --git a/website/version2/examples/examples3.html b/website/version2/examples/examples3.html new file mode 100755 index 0000000..b64aac3 --- /dev/null +++ b/website/version2/examples/examples3.html @@ -0,0 +1,78 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+

Jalview will search Uniprot to find the exact protein + sequence match from any input alignment file. This can be used to display + sequence features, moving the mouse over the displayed feature will + reveal more information.

+

+


+ Jalview allows the alignment to be "wrapped"

+

+

< + Back    Next >

+ +
+
+ + diff --git a/website/version2/examples/examples4.html b/website/version2/examples/examples4.html new file mode 100755 index 0000000..043bb8a --- /dev/null +++ b/website/version2/examples/examples4.html @@ -0,0 +1,84 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+ Many new features have been added to the Jalview interface, + such as the Overview window which aids navigation around the whole alignment. +

+


+ Search using regular expressions.

+

+ The functionality of the original Jalview has been maintained + and enhanced in the new interface. Below is an example of an average + distance tree, calculated from the input alignment, being used to cluster + sequences in the main alignment window.
+ The user has then applied "Conservation Colouring" to the + alignment, the result of which shows conservation within the clustered + sequences. +

< + Back      Next + >

+ +
+
+ + diff --git a/website/version2/examples/examples5.html b/website/version2/examples/examples5.html new file mode 100755 index 0000000..acc8a35 --- /dev/null +++ b/website/version2/examples/examples5.html @@ -0,0 +1,78 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+

Jalview maintains the ability to perform Principal Component + Analysis on an alignment. The method is used to cluster similar sequences, + the user may then select sequences from this 3D visual display.

+

+


+ PDB structures may be displayed if Jalview can find a match of the input + sequence and Uniprot.

+

+

< + Back

+ +
+
+ + diff --git a/website/version2/examples/globins.jar b/website/version2/examples/globins.jar new file mode 100755 index 0000000..a0d70eb Binary files /dev/null and b/website/version2/examples/globins.jar differ diff --git a/website/version2/examples/glut.msf b/website/version2/examples/glut.msf new file mode 100755 index 0000000..0c9c83c --- /dev/null +++ b/website/version2/examples/glut.msf @@ -0,0 +1,299 @@ +PileUp + + + + MSF: 439 Type: P Check: 2277 .. + + Name: AJPMQA oo Len: 439 Check: 4128 Weight: 1.00 + Name: AJFBQA oo Len: 439 Check: 6903 Weight: 1.00 + Name: AJAAQ oo Len: 439 Check: 4168 Weight: 1.00 + Name: AJFBQB oo Len: 439 Check: 5921 Weight: 1.00 + Name: AJPMQ1 oo Len: 439 Check: 4951 Weight: 1.00 + Name: AJFBQ oo Len: 439 Check: 7754 Weight: 1.00 + Name: AJYLNB oo Len: 439 Check: 1096 Weight: 1.00 + Name: AJRZQG oo Len: 439 Check: 7565 Weight: 1.00 + Name: AJLCQB oo Len: 439 Check: 5610 Weight: 1.00 + Name: AJRZQB oo Len: 439 Check: 5547 Weight: 1.00 + Name: AJFBQD oo Len: 439 Check: 2775 Weight: 1.00 + Name: AJPMQ2 oo Len: 439 Check: 3516 Weight: 1.00 + Name: AJRZQD oo Len: 439 Check: 1469 Weight: 1.00 + Name: AJBHQ oo Len: 439 Check: 2409 Weight: 1.00 + Name: AJDHQ oo Len: 439 Check: 5591 Weight: 1.00 + Name: AJMSQ oo Len: 439 Check: 9358 Weight: 1.00 + Name: AJMSQ3 oo Len: 439 Check: 166 Weight: 1.00 + Name: AJHYQ oo Len: 439 Check: 415 Weight: 1.00 + Name: AJRTQ oo Len: 439 Check: 9855 Weight: 1.00 + Name: AJHUQ oo Len: 439 Check: 1969 Weight: 1.00 + Name: AJCHQ oo Len: 439 Check: 7657 Weight: 1.00 + Name: AJFF2C oo Len: 439 Check: 4626 Weight: 1.00 + Name: AJFF1M oo Len: 439 Check: 6582 Weight: 1.00 + Name: AJSM2V oo Len: 439 Check: 8742 Weight: 1.00 + Name: AJSM2H oo Len: 439 Check: 4241 Weight: 1.00 + Name: AJKXQ oo Len: 439 Check: 5092 Weight: 1.00 + Name: AJZJQ2 oo Len: 439 Check: 4171 Weight: 1.00 + +// + + + +AJPMQA .......... .......... .......... .......... .......... +AJFBQA .......... .......... .......... .......... .......... +AJAAQ .......... .......... .......... .......... .......... +AJFBQB .......... .......... .......... .......... .......... +AJPMQ1 .......... .......... .......... .......... .......... +AJFBQ .......... .......... .......... .......... .......... +AJYLNB .......... .......... .......... .......... .......... +AJRZQG .......... .......... .......... .......... .......... +AJLCQB .......... .......... .......... .......... .......... +AJRZQB .......... .......... .......... .......... .......... +AJFBQD ........MA QILAPSTQWQ MRFTKSSRHA SPITSNTWSS LLMKQNKK.T +AJPMQ2 ........MA QILAPSTQWQ MRITKTSPCA TPITSKMWSS LVMKQTKKVA +AJRZQD ......MAQA VVPAMQCQVG AVR....ARP AAAAAAAGGR VWGVRRTGRG +AJBHQ ....MQVRRD DDGAGGCAGD AVPGGGEGQD GVPARQPAGR VWGVSRAARA +AJDHQ .......... .......... .......... .......... .......... +AJMSQ .......... .......... .......... .......... .......... +AJMSQ3 .......... .......... .......... .......... .......... +AJHYQ .......... .......... .......... .......... .......... +AJRTQ .......... .......... .......... .......... .......... +AJHUQ .......... .......... .......... .......... .......... +AJCHQ .......... .......... .......... .......... .......... +AJFF2C .......... .......... .......... .......... .......... +AJFF1M .......... .......... ...MALRVAG LFLKKELVAP ATQQLRLLRT +AJSM2V .......... .......... .......... .......... .......... +AJSM2H .......... .......... .......... .......... .......... +AJKXQ .......... .......... .......... .......... .......... +AJZJQ2 .......... .......... .......... .......... .......... + + +AJPMQA .......... ....MSSLSD LINFNLSDST EKIIAEYIWV GGS..GIDIR +AJFBQA .......... ....MSLLSD LINLNLSEST EKIIAEYIWV GGS..GMDLR +AJAAQ .......... ....MSLLSD LINLDLSETT EKIIAEYIWI GGS..GLDLR +AJFBQB .......... ....MSLLSD LINLNLSDTT EKVIAEYIWI GGS..GLDLR +AJPMQ1 .......... .....MSLSD LINLDLSGTT EKIIAEYIWI GGS..GLDLR +AJFBQ .......... ....MSSISD LVNLNLSDST ERVIAEYIWV GGS..GMDMR +AJYLNB .......... ....MSLLSD LINLNLSDTT EKIIAEYIWV GGS..GVDLR +AJRZQG .......... ....MASLTD LVNLNLSDTT EKIIAEYIWI GGS..GMDLR +AJLCQB .......... ....MALLSD LVNLDLSSIN DKIIAEYIWI GGS..GMDLR +AJRZQB .......... ....MANLTD LVNLNLSDCS DKIIAEYIWV GGS..GIDLR +AJFBQD SSFRVLAVKS DGSTINRLEG LLNLDITPFT DKIIAEYIWI GGT..GIDVR +AJPMQ2 HSFRVMAVNS ENGTINRVED LLNLDITPFT DSIIAEYIWI GGT..GIDVR +AJRZQD TSRVMAVSTE TTGVVTRMEQ LLNMDTTPFT DKIIAEYIWV GGT..GIDLR +AJBHQ TSKVLALGPE TTGVIQRMQQ LLDMDTTPFT DKIIAEYIWV GGS..GIDLR +AJDHQ .......... .......... .......... .......... .......... +AJMSQ ......MATS ASSHLNKGIK QMYMSLPQGE .KVQAMYIWV DGT..GEGLR +AJMSQ3 ......MATS ASSHVNKGIK QMYMSLPQGE .KIQAMYIWV NGT..GEPLR +AJHYQ ......MATS ASSHLNKNIK QMYLCLPQGE .KVQAMYIWV DGT..GEGLR +AJRTQ ......MATS ASSHLNKGIK QMYMNLPQGE .KIQLMYIWV DGT..GEGLR +AJHUQ ......MTTS ASSHLNKGIK QVYMSLPQGE .KVQAMYIWI DGT..GEGLR +AJCHQ ......MATS ASSHLSKAIK HMYMKLPQGE .KVQAMYIWI DGT..GEHLR +AJFF2C ..SARILEDS PNARINKTIL DRYLSLPLQE NIVQATYVWI DGT..GEDLR +AJFF1M GNRSQFLANS PNTALDKSIL QRYRNLETPA NRVQATYLWI DGT..GENIR +AJSM2V .......... .......... .......... MTFKAEYIWI DGTEPTAKLR +AJSM2H .......... .......... .......... MSIKAEYIWI DGTQPTAKLR +AJKXQ .......... .......... .......... MSYQAEYIWI DGTEPEPLMR +AJZJQ2 .......... .......... .........M TKYKLEYIWL DGYTPTPNLR + + +AJPMQA AR.TLPGPVS DPAKLPKWNY DGSSTNQAPG KDSEVILYPQ AIFKDPFR.N +AJFBQA AR.TLPGPVD DPAKLPKWNY DGSSTDQAPG DDSEVILYPQ AIFKDPFR.N +AJAAQ AR.TLPGPVT DPSQLPKWNY DGSSTGQAPG EDSEVIIYPQ AIFKDPFR.N +AJFBQB AR.TLPGPVK NPSELPKWNY DGSSTGQAPG QDSEVIIYPQ AIFKDPFR.N +AJPMQ1 AR.TLPGPVT DPSELPKWNY DGSSTGQAPG QDSEVILYPQ AIFKDPFR.N +AJFBQ AR.TLSGPVK DPSKLPKWNY DGSSTGQAPG QDSEVILYPQ TIFRDPFR.N +AJYLNB AR.TLSGPVN DPSKLPKWNY DGSSTGQAPG KDSEVILWPQ AIFKDPFR.N +AJRZQG AR.TLSGPVT DPSKLPKWNY DGQAPGQAPG EDSEVILYPQ AIFKDPFR.N +AJLCQB AR.TISRPVS .DPSELPKWN YDGSSTGQAP GEDSEVIIYP QAIFKDPFKN +AJRZQB AR.TVKGPIT DVSQLPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.D +AJFBQD SR.TISKPVE HPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N +AJPMQ2 SR.TISKPVS HPSEVPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N +AJRZQD SR.TISKPVE DPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N +AJBHQ SR.TISKPVE DPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N +AJDHQ .......... .......... .......... .......... .......... +AJMSQ TR.TLDCEPK CVEELPEWNF DGSSTFQSEG SNSDMYLHPV AMFRDPFR.P +AJMSQ3 TCRTLDCEPK CVEELPEWNF DGSSTFQSEG SNSNMYLHPV AMFRDPFR.. +AJHYQ TR.TLDCEPK CVEELPEWNF DGSSTFQSEG SNSDMYLSPV AMFRDPFR.P +AJRTQ TR.TLDCDPK CVEELPEWNF DGSSTFQSEG SNSDMYLHPV AMFRDPFR.P +AJHUQ TR.TLDSEPK CVEELPEWNF DGSSTLQSEG SNSDMYLVPA AMFRDPFR.P +AJCHQ TR.TLDHEPK SLEDLPEWNF DGSSTFQAEG SNSDMYLRPA AMFRDPFR.P +AJFF2C DR.TLDFIPQ SPKELPVWNY DGSSCYQAEG SNSDTYLYPV AIYKDPFR.N +AJFF1M DR.VLDKVPS SVEDLPDWQY DGSSTYQAHG ENSDTTLKPR AIYRDPFKKN +AJSM2V TKIITGQPAG .LDALPIWGF DGSSTNQAEG HSSDCVLKPV FTCPDPIRGD +AJSM2H TKILSDGSR. ....LPRWGF DGSSTNQAEG HASDLVLEPV FSCPDPIRGD +AJKXQ TRIIKDGKE. ....PEIWGF DGSSTNQAPG SNSDCVLRPV FETPDPIRGD +AJZJQ2 TQIKEFASFP TLEHVPLWGF DGSSTQQAEG HSSDCVLKPV AVFPDAARTN + + +AJPMQA NILVICDVYT PAGEP.LPTN KRYNAAKIFS HPDVAAEVPW YGIEQELLQK +AJFBQA NILVICDVYT PAGEP.LPTN KRYDAAKIFS HPDVVAEVPW YGIEQELLQK +AJAAQ NILVMCDAYT PAGEP.IPTN KRHAAAKIFS HPDVVAEVPW YGIEQELLQK +AJFBQB NILVICDAYT PAGEP.IPTN KRHNAAKIFS NPDVVAEEPW YGIEQELLQK +AJPMQ1 HILVMCDAYS PAGEP.IPTN KRHAAAKVFS HPDVVAEETW YGIEQELLQK +AJFBQ NILVMCDAYT PAGEP.IPTN KRHNAAKIFS NPEVVAEEPW YGIEQELLQK +AJYLNB NILVICDTYT PSGKP.IPTN KRHAAAKIFS HPDVAAEEPW FGIEQELLQK +AJRZQG NILVMCDCYT PAGEP.IPTN KRHNAAKIFS SPEVASEEPW YGIEQELLQK +AJLCQB HILVMCDAYT PAGEP.IPTN KRAAAAKIFS NPEVEKEVTW YGIEQELLQK +AJRZQB NILVMCDCYT PQGEP.IPTN KRHSAAKIFS HPDVVAEVPW YGIEQELLQK +AJFBQD NILVICDAYT PAGEP.IPTN KRHRAAEVFS NPRVIAEVPW FGIEQELLQT +AJPMQ2 NILVVCDAYT PAGEP.IPTN KRHRAAEIFS NPKVEAEIPW YGIEQELLQT +AJRZQD NILVMCDTYT PAGEP.IPTN KRNRAAQVFS DPKVVSQVPW FGIEQELLQR +AJBHQ NILVICDTYT PQGEP.IPTN KRHMAAQIFS DPKVTSQVQW FGIEQELMQR +AJDHQ .......... .......... .......... ....KAQEPW FGIEQELLNS +AJMSQ NKLVLCEVFK YNRKP.AETN LRH..ICKRI MDMVSNQHPW FGMEQELMGT +AJMSQ3 NKLVLCEVFK YNRKP.AETN LRH..ICKRI MDMVSNQHPW FGMEQELMGT +AJHYQ NKLVFCEVFK YNRKP.AETN LRH..SCKRI MDMVSNQHPW FGMEQELMGT +AJRTQ NKLVFCEVFK YNRKP.AETN LRH..SCKRI MDMVSSQHPW FGMEQELMGT +AJHUQ NKLVLCEVFK YNRRP.AETN LRH..TCKRI MDMVSNQHPW FGMEQELMGT +AJCHQ NKLVLCEVFK YNRQS.ADTN LRH..TCRRI MDMVSNQHPW FGMEQELLGT +AJFF2C NILVMCDTYK FDGTP.TDTN KRK..TCLEV ANKCAAEEPW FGIEQESDFD +AJFF1M DVIVLCDTYS ADGKP.TASN KRA..AFQAA IDLISDQEPW FGIEQELLRR +AJSM2V DILVLCEVLN IDLTPH.ASN TRAALAEVAE RFAA..QEPI FGIEQEFFQD +AJSM2H HLLVLCEVLH TDLTPH.PSN TRALLRPVAE RFAG..QEPI FGIEQEFLKG +AJKXQ NRLVLCEVQL TDFTP..PTN TRAAALGVAE RYAD..MSPM FGIEQEFFKD +AJZJQ2 GVLVMCEVMM PDGKTPHASN KRATILDDAG ........AW FGFEQEFYKD + + +AJPMQA DINWPLGWPI GG..YPGKQG PYYCGIGADK AY..GRDIVD AHYKAFAGIN +AJFBQA DVNWPLGWPL GG..YPGPQG PYYCGVGADK AY..GRDIVD AHYKAYAGIN +AJAAQ DINWPLGWPV GG..FPGPQG PYYCGAGADK AF..GRDIVD SHYKAYAGIN +AJFBQB EVNWPVGWPV GG..FPGPQG PYYCGVGADK AF..GRDIVD AHYKAYAGIN +AJPMQ1 DINWPLGWPA GG..YPGPQG PYYCSVGADK AF..GRDVVE AHYKAFAGIN +AJFBQ DVQWPVGWPL GG..FPGPQG PYYCGIGANK AF..GRDIVD SHYKAYAGIN +AJYLNB DIHWPIGMAL GG..FPGPQG PYYCGTGAEK AF..GRDIVD SHYKAYAGIN +AJRZQG DINWPLGWPV GG..FPGPQG PYYCGIGADK SF..GRDIVD SHYKAYAGIN +AJLCQB DTNWPLGWPL GG..FPGPQG PYYCGIGADK AF..GRDIVH AHYKAYAGVN +AJRZQB DVNWPLGWPV GG..FPGPQG PYYCAAGAEK AF..GRDIVD AHYKAYAGIN +AJFBQD NVNWPLGWPV GG..YPGPQG PYYCSAGADK SF..GRDISD AHYKAFAGIN +AJPMQ2 NVKWPLGWPV GG..YPGPQG PYYCAAGADK SF..GRDISD AHYKAYAGIN +AJRZQD DVNWPLGWPV GG..YPGPQG PYYCAVGSDK SF..GRDISD AHYKAYAGIN +AJBHQ DVNWPLGWPV GG..YPGPQG PYYCAVGSDK SF..GRDISD AHYKAYAGIE +AJDHQ VTKWPLGWPK GG..YPAGQG PYYCSVGAGR SI..GRDIPE VHYRCHAGIQ +AJMSQ DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK +AJMSQ3 DG.HPFGWPF NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK +AJHYQ DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK +AJRTQ DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGIK +AJHUQ DG.HPFGWPS NG..FPGPQG PYYCGVGADR AY..GRDIVE AHYRAYAGVK +AJCHQ DG.HPFGWPS NC..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK +AJFF2C G....HHWAG QEW.FPDP.G PYYCGVGANK SS..PR.HKD AHYAPYAGTQ +AJFF1M GR.TSFGWPE NG..FPAPQG PYYCGVGADR VY..ARDLVE AHVVAYAGID +AJSM2V GY..PLGFPK GG..FPAPQG GYYCGVGADE IF..GRDVVE AHLDNKAGLA +AJSM2H DR..PLGFPE GGG.YPAPQA DYYCGVGADA IF..GREIVE KHLDLAAGLG +AJKXQ GR..PYGWPE VG..YPAPQG PYYCGVGGSK MP..GRQIVE RHTQADAGLA +AJZJQ2 GR..PLGFPT SG..YPAPQG PYYTGVGFSN VGDVARKIVE EHLDLAAGIN + + +AJPMQA ISGINGEVMP GQWEFQVGPS VGISAGDEIW AARYILERIT EIAVVSFDPK +AJFBQA ISGINGEVMP GQWEFQVGPS VGISAGDEVW AARYILERIT ELAVVSFDPK +AJAAQ ISGINGEVMP GQWEFQVGPS VGISAGDEIW VARYILERIT EVAVLSFDPK +AJFBQB ISGINGEVMP GQWEFQVGPA VGISAGDELW VARYILERIT EVAVLSFDPK +AJPMQ1 ISGINGEVMP GQWEFQVGPS VGISAGDEIW VARYILERIT EVAVLTFDPK +AJFBQ ISGINGEVMP GQWEFQVGPS VGISAADELW VARYILERIT EIAVLSFDPK +AJYLNB ISGINAEVMP GQWEFQVGPS IGISAGDELW VARYILERIT EIAVLSLDPK +AJRZQG ISGINGEVMP GQWEFQVGPS VGISAGDQVW VARYILERIT EIAVVSFDPK +AJLCQB ISGINGEVMP GQWEFQVGPS VGIAAADQIW VARYILERIT EIYVVSFDPK +AJRZQB ISGINGEVMP GQWEFQVGPS VGIAAADQVW VARYILERVT EVAVLSLDPK +AJFBQD ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ASRYILERIT EQAVLSLDPK +AJPMQ2 ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ASRYILERIT EQAVLTLDPK +AJRZQD ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ISRYILERIT EQAVLTLDPK +AJBHQ ISGTNGEVMP GQWEYQVGPS VGIDAGDHIW ASRYILERIT EQAVLTLDPK +AJDHQ ISGVNGEVLP SQWEYQVGPV EGIAMGDQMW MSRYLMYRVA ELFEVTFDPK +AJMSQ ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW IARFILHRVC EDFIATFDPK +AJMSQ3 ITGTNAEVMP AQW....... .......... .......... .......... +AJHYQ ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW VARFILHRVC EDFIATFDPK +AJRTQ ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW VARFILHRVC EDFIATFDPK +AJHUQ IAGTNAEVMP AQWEFQIGPC EGISMGDHLW VARFILHRVC EDFIATFDPK +AJCHQ IGGTNAEVMP AQWEFQVGPC EGIEMGDHLW IARFILHRVC EDFIVSFDPK +AJFF2C GVPTNAEVMP AQWEFQVGPC EGISIGDDLW MARFLLHRIS EEFVSTLDPK +AJFF1M FAGTNAEVMP AQWEFQIGPA G.IKACDDLW VSRYILQRIA EEYVVTFDPK +AJSM2V ISGINAEVMP GQWEFQVGPV SPLEVSDHLW VARWLLYRTA EDFAATLDPK +AJSM2H LSGINAEVMP GQWEFQVGAL PPLEVSDHMW VARWLLHRVA EEFTASLDAK +AJKXQ IEGTNAEVMM GQWEFQIGVL PAPAIGDQIW LGRWLLHRIA EDYEVSFAAK +AJZJQ2 HEGINAEVAK GQWEFQIFGK GSKKAADEMW MARYLMLRLT EKYDIEFHCK + + +AJPMQA PIPG.DWNGA GAHANFSTKS MRENGGYEVI KKAIEKLGLR HHIAAYGE.. +AJFBQA PIPG.DWNGA GAHSNYSTKS MREEGGYEVI KKAIEKLGLR HHIAAYGK.. +AJAAQ PIKG.DWNGA GAHTNYSTKS MREDGGYEVI LKAIEKLGKK HHIAAYGE.. +AJFBQB PIKG.DWNGA GAHTNYSTKT MRNDGGYEEI KSAIQKLGKR HHIAAYGE.. +AJPMQ1 PIKG.DWNGA GAHTNYSTKS MREDGGYEII KKAIEKLGKR LHISAYGE.. +AJFBQ PIQG.DWNGA GAHTNYSTKS MRNDGGYEVI KKAITKLEKR HHIAAYGE.. +AJYLNB PIPG.DWNGA GAHTNYSTKS MRNDGGYEVI KQAIEKLEKR HHIAAYGE.. +AJRZQG PIPG.DWNGA GAHTNYSTKS MRNDGGYEII KSAIEKLKLR HHISAYGE.. +AJLCQB PIPG.DWNGA GAHTNYSTKT MREEGGYEVI KKAIEKLGLR HHIAAYGE.. +AJRZQB PIPG.DWNGA GAHTNFSTKS MREPGGYEVI KKAIDKLALR HHIAAYGE.. +AJFBQD PIEG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHISAYGE.. +AJPMQ2 PIEG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHIEAYGE.. +AJRZQD PIQG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHISAYGE.. +AJBHQ PIQG.DWNGA GCHTNYSTLS MREDGGFDVI KKAILNLSLR HHIAAYGE.. +AJDHQ PIPG.DWNGS GGHVNFSNRQ PESPPAGKQS RSSAKKLGKR HHIAAYGE.. +AJMSQ PIPG.NWNVA GCHTNFSTKA MREENGLKCI EEAIDKLSKR HHIRAYDPKG +AJMSQ3 .......... .......... .......... .......... .......... +AJHYQ PIPG.NWNGA GCHTNFSTKA MREENGLKHI EEAIEKLSKR HHIRAYDPKG +AJRTQ PIPG.NWNGA GCHTNFSTKA MREENGLRCI EEAIDKLSKR HHIRAYDPKG +AJHUQ PIPG.NWNGA GCHTNFSTKA MREENGLKYI EEAIEKLSKR HHIRAYDPKG +AJCHQ PIPG.NWNGA GCHTNFSTKN MREDGGLKHI EEAIEKLSKR HHIRAYDPKG +AJFF2C PMPG.DWNGA GAHTNVSTNA MREDGGIRDI EKAVAKLSKC HHIRAYDPKQ +AJFF1M PMEG.QWNGA GAHTNFSTKE MRADGGIKAI EEAIEKLSKR HHIKAYYPKE +AJSM2V PVKG.DWNGA GAHTNFSTKA MRESYDAIIT AAESLGEGSK PHVKNYGA.. +AJSM2H PAKG.DWNGA GAHTNFSTRA MREGYDPIIT ACEALGQDDK PHVRQYGT.. +AJKXQ PIPG.DWNGA GAHTNFSTKQ TMEGWDAIVT CCEALG..TR VHVTHYGK.. +AJZJQ2 PLGDTDWNGS GMHANFSTEY MRTVGGKEYF EALMAAFDKN LHIAVYGP.. + + +AJPMQA ..GNERRLTG KHETADINVF SWGVANRGSS IRVGRDTEKG KGYFEDRRPA +AJFBQA ..GNERRLTG RHETADINTF SWGVANRGSS VRVGRDTEKG KGYFEDRRPA +AJAAQ ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPS +AJFBQB ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPA +AJPMQ1 ..GNERRLTG KHETADINTF SWGVANRGAS VRVGRDTEKG KGYFEDRRPA +AJFBQ ..GNERRLTG KHETADMNTF IWGVANRGAS IRVGRDTEKG KGYFEDRRPA +AJYLNB ..GNERRLTG RHETADISTF SWGVANRGAS I......... .......... +AJRZQG ..GNERRLTG RHETADINTF SWGVANRGAS VRVGRETEQG KGYFEDRRPA +AJLCQB ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPA +AJRZQB ..GNERRLTG RHETADINTF KWGVANRGAS IRVGRDTEKG KGYFEDRRPA +AJFBQD ..GNERRLTG KHETASINTF SWGVANRGCS IRVGRDTEKG KGYLEDRRPA +AJPMQ2 ..GNERRLTG KHETASINDF SWGVANRGCS IRVGRDTEKG KGYLEDRRPA +AJRZQD ..GNERRLTG LHETASIDNF SWGVANRGCS IRVGRDTEAG KGYLEDRRPA +AJBHQ ..GNERRLTG LHETASISDF SWGVANRGCS IRVGRDTEAG KGYLEDRRPA +AJDHQ ..GNERRLTG KHETSSMNDF SWGVANRGCS IRVGRMVPVK CGYYEDRRPS +AJMSQ GLDNARALTG FHETSNINDF SAGVANRGAS IRIPRTVGQK KGYFEDRRLR +AJMSQ3 .......... .......... .......... .......... .......... +AJHYQ GLDNARGLTG FHETSNINDF SAGVANRSAS IRIPRTVGQK KGYFEDRRPS +AJRTQ GLDNARRLTG FHETSNINDF SAGVANRSAS IRIPRIVGQK KGYFEDRRPS +AJHUQ GLDNARRLTG FHETSNINDF SAGVANRSAR LRIPRTVGQK KGYFEDRRPS +AJCHQ GLDNARRLTG FHETSSIHEF SAGVANRGAS IRIPRNVGHK KGYFEDRGPS +AJFF2C GQDNARRLTG KHETSSINDF SAGVANRGCS IRIPRGVNDG KGYFEDRCPS +AJFF1M GKDNERRLVG RLETSSIDKF SWGVANRAVS VRVPRGVATG KGYLEDRRPS +AJSM2V ..GIDDRLTG LHETAPWNEY SYGVSDRGAS VRIPWQVEKG KGYIEDRRPN +AJSM2H ..GIEDRLTG AHETAPWDAY SYGASDRGAS VRIPWQVEVK KGYIEDRRPN +AJKXQ ..GIEDRLTG KHETAPWNKY SWGASDRGAS VRIPWAVEKK KGWLEDRRPN +AJZJQ2 ..DNDKRLTG KHETAPWNKF SYGVADRGAS IRVPHSFVNY KGYLEDRRPN + + +AJPMQA SNMDPYVVTS MIAETTILWK KP........ ......... +AJFBQA SNMDPYVVTS MIAETTILWK P......... ......... +AJAAQ SNMDPYVVTS MIADTTILWK P......... ......... +AJFBQB SNMDPYVVTS MIADTTILWK P......... ......... +AJPMQ1 SNMDPYVVTS MIAETTILLK P......... ......... +AJFBQ SNMDPYVVTS MIAETTLLWK P......... ......... +AJYLNB .......... .......... .......... ......... +AJRZQG SNMDPYIVTS MIAETTIIWK P......... ......... +AJLCQB SNMDPYVVTS MIAETTILWD NKS....... ......... +AJRZQB SNMDPYVVTG MIAETTLLWK QN........ ......... +AJFBQD SNMDPYVVTS LLAESTLLWE PTLEAEALAA QKLALKV.. +AJPMQ2 SNMDPYVVTA LLAESTLLWE PTLEAEALAA QKIALKV.. +AJRZQD SNMDPYVVTA LLAETTILWE PTLEAEVLAA KKLALKV.. +AJBHQ SNMDPYTVTA LLAETTILWE PTLEAEALAA KKLALKV.. +AJDHQ SNLDPYVVTR LLVETTLL.. .......... ......... +AJMSQ ANCDPYAVTE AIVRTCLLNE TGDEPFQYKN ......... +AJMSQ3 .......... .......... .......... ......... +AJHYQ ANCDPFAVTE AIVRTCLLNE TGDEPFQYKN ......... +AJRTQ ANCDPYAVTE AIVRTCLLNE TGDEPFQYKN ......... +AJHUQ ANCEPFSVTE ALIRTCLLNE TGDEPFQYKN ......... +AJCHQ ANCDPYAVTE ALVRTCLLNE TGDEPFEYKN ......... +AJFF2C SNCDPYSVVE AILRTICLDE .......... ......... +AJFF1M SNCDPYAVCN AIVRTCLLNE .......... ......... +AJSM2V ANVDPYVVTR LLVDTCCSAL EK.......A GQV...... +AJSM2H ANVDPYVVTR LMVDTCCTEL AR.......R EQI...... +AJKXQ ANMDPYLVTA LMIDTCCSAL AGDKPTLFVP SQTTPAPAS +AJZJQ2 SQGDPYQIVR RS........ .......... ......... + + diff --git a/website/version2/examples/glut.newick b/website/version2/examples/glut.newick new file mode 100755 index 0000000..d1f965b --- /dev/null +++ b/website/version2/examples/glut.newick @@ -0,0 +1 @@ +((AJRZQB:6.0347505,(AJRZQG:5.005189,(AJFBQ:5.0496607,(AJYLNB:4.8739843,((((((AJZJQ2:17.922678,(AJKXQ:13.302137,(AJSM2H:9.190935,AJSM2V:8.348928):4.237726):4.1729946):2.1668549,((AJFF1M:17.32338,AJFF2C:14.795074):1.1247139,(AJMSQ3:0.0,(AJCHQ:4.7881308,(AJHUQ:3.5035172,(AJRTQ:1.5708065,(AJHYQ:1.594532,AJMSQ:1.8223228):0.25151634):1.0522919):2.2449017):4.756546):6.748291):0.93679047):2.2975445,AJDHQ:3.1142578):7.6872816,(AJBHQ:6.8556995,AJRZQD:5.6727734):4.075513):0.63313675,(AJPMQ2:4.3359585,AJFBQD:3.6367054):5.6366634):2.04666,((AJPMQ1:4.699384,(AJFBQB:3.4119358,AJAAQ:2.5106182):0.31200266):0.88102937,(AJFBQA:2.4191017,AJPMQA:3.2756615):2.5073526):0.42850304):0.0):0.0):0.26338387):0.46177864):6.5498247,AJLCQB:6.5498247); diff --git a/website/version2/examples/jalviewlite.jar b/website/version2/examples/jalviewlite.jar new file mode 100755 index 0000000..99b506e Binary files /dev/null and b/website/version2/examples/jalviewlite.jar differ diff --git a/website/version2/examples/jpred.jpg b/website/version2/examples/jpred.jpg new file mode 100755 index 0000000..011c982 Binary files /dev/null and b/website/version2/examples/jpred.jpg differ diff --git a/website/version2/examples/jpredQ.jpg b/website/version2/examples/jpredQ.jpg new file mode 100755 index 0000000..8e1a4b7 Binary files /dev/null and b/website/version2/examples/jpredQ.jpg differ diff --git a/website/version2/examples/lipase.msf b/website/version2/examples/lipase.msf new file mode 100755 index 0000000..f737753 --- /dev/null +++ b/website/version2/examples/lipase.msf @@ -0,0 +1,207 @@ +PileUp + + + + MSF: 487 Type: P Check: 4627 .. + + Name: LIP1_CANFA oo Len: 487 Check: 678 Weight: 1.00 + Name: LIP2_MOUSE oo Len: 487 Check: 2632 Weight: 1.00 + Name: LIPH_HUMAN oo Len: 487 Check: 2807 Weight: 1.00 + Name: LIPH_MOUSE oo Len: 487 Check: 1096 Weight: 1.00 + Name: LIPH_RAT oo Len: 487 Check: 1917 Weight: 1.00 + Name: LIPL_BOVIN oo Len: 487 Check: 3520 Weight: 1.00 + Name: LIPL_CAVPO oo Len: 487 Check: 9282 Weight: 1.00 + Name: LIPL_CHICK oo Len: 487 Check: 7040 Weight: 1.00 + Name: LIPL_HUMAN oo Len: 487 Check: 3879 Weight: 1.00 + Name: LIPL_MOUSE oo Len: 487 Check: 5123 Weight: 1.00 + Name: LIPL_RAT oo Len: 487 Check: 3636 Weight: 1.00 + Name: LIPP_HORSE oo Len: 487 Check: 3071 Weight: 1.00 + Name: LIPP_HUMAN oo Len: 487 Check: 243 Weight: 1.00 + Name: LIPP_PIG oo Len: 487 Check: 3267 Weight: 1.00 + Name: LIPP_RABIT oo Len: 487 Check: 5962 Weight: 1.00 + Name: LIPP_RAT oo Len: 487 Check: 474 Weight: 1.00 + +// + + + +LIP1_CANFA KEVCYEQIGC FSDAEPWAG. TAIRPLKVLP WSPERIGTRF LLYTNKNP.N +LIP2_MOUSE KEVCYGHLGC FSNDKPWAG. MIQRPSKIFP WSPEDIDTRF LLYTNENP.N +LIPH_HUMAN SSALGQSLKP EPFGRRAQA. ......VETN KTLHEMKTRF LLFGETN... +LIPH_MOUSE SSACGQGVGT EPFGRSLGA. ......TEAS KPLKKPETRF LLFQDEND.R +LIPH_RAT SSACGQGVGT EPFGRNLGA. ......TEER KPLQKPEIRF LLFKDESD.R +LIPL_BOVIN LDPAGPNFEY AEDRITGG.. .......... KDFRDIESKF ALRTPEDTAE +LIPL_CAVPO MNIDRKILNK ALAKEKVAN. ........CQ KDYTDIESKF ARRTPENTVE +LIPL_CHICK KTALLAVLCL CLRGAAGSD. ......PEAE MNFEGIESKF SLRTPAEPDE +LIPL_HUMAN LAVWLQSLTA SRGGVAAAD. ........QR RDFIDIESKF ALRTPEDTAE +LIPL_MOUSE LGVWLQSLTA FRGGVAAAD. ........AG RDFSDIESKF ALRTPEDTAE +LIPL_RAT LGVWLQSLTA FRGGVAAAD. ........GG RDFSDIESKF ALRTPEDTAE +LIPP_HORSE NEVCYERLGC FSDDSPWAG. IVERPLKILP WSPEKVNTRF LLYTNENP.D +LIPP_HUMAN KEVCYERLGC FSDDSPWSG. ITERPLHILP WSPKDVNTRF LLYTNENP.N +LIPP_PIG SEVCFPRLGC FSDDAPWAG. IVQRPLKILP PD.KDVDTRF LLYTNQNQ.N +LIPP_RABIT LEVCYERLGC FGNRIPWSGG TLERPFSTLP STPKIVNTRF LLYTNENP.N +LIPP_RAT KEVCFDKLGC FSDDAPWSG. TIDRPLKALP WSPAQINTRF LLYTNENQ.D + + +LIP1_CANFA NFQTLLPSDP STIEASNFQT DKKTRFIIHG FIDKGE.ENW LLDMCKNMFK +LIP2_MOUSE NYQIISATDP ATINASNFQL DRKTRFIIHG FIDKGE.EGW LLDMCKKMFQ +LIPH_HUMAN QGCQIRINHP DTLQECGFNS SLPLVMIIHG WSVDGVLENW IWQMVAALKS +LIPH_MOUSE LGCRLRPQHP ETLQECGFNS SQPLIMIIHG WSVDGLLENW IWKIVSALKS +LIPH_RAT LGCQLRPQHP ETLQECGFNS SHPLVMIIHG WSVDGLLETW IWKIVGALKS +LIPL_BOVIN DTCHLIPGVT ESVANCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK +LIPL_CAVPO DTCHLIPGVT ESVANCHFNH SSKTFMVIHG WTVTGMYESW VPKLVAALYK +LIPL_CHICK DVCYLVPGQM DSLAQCNFNH TSKTFVVIHG WTVTGMYESW VPKLVDALYK +LIPL_HUMAN DTCHLIPGVA ESVATCHFNH SSKTFMVIHG WTVTGMYESW VPKLVAALYK +LIPL_MOUSE DTCHLIPGLA DSVSNCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK +LIPL_RAT DTCHLIPGLA DSVSNCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK +LIPP_HORSE NFQEIV.ADP STIQSSNFNT GRKTRFIIHG FIDKGE.ESW LSTMCQNMFK +LIPP_HUMAN NFQEVA.ADS SSISGSNFKT NRKTRFIIHG FIDKGE.ENW LANVCKNLFK +LIPP_PIG NYQELV.ADP STITNSNFRM DRKTRFIIHG FIDKGE.EDW LSNICKNLFK +LIPP_RABIT NFQEIS.ADA STIRGSNFRT DRKTRFIIHG FTDKGE.ENW LSNLCENLFQ +LIPP_RAT NYQKIT.SDA SSIRNSNFKT NRKTRIIIHG FIDKGE.ENW LSDMCKNMFK + + +LIP1_CANFA V...EEVNCI CVDWKKGSQT SYTQAANNVR VVGAQVAQML SMLSANYSYS +LIP2_MOUSE V...EKVNCI CVDWKRGSRT EYTQASYNTR VLGAEIAFLV QVLSTEMGYS +LIPH_HUMAN QPAQP.VNVG LVDWITLAHD HYTIAVRNTR LVGKEVAALL RWLEESVQLS +LIPH_MOUSE RQSQP.VNVG LVDWISLAYQ HYTIAVQNTR IVGQDVAALL LWLEESAKFS +LIPH_RAT RQSQP.VNVG LVDWISLAYQ HYAIAVRNTR VVGQEVAALL LWLEESMKFS +LIPL_BOVIN R..EPDSNVI VVDWLSRAQQ HYPVSAGYTK LVGQDVAKFM NWMADEFNYP +LIPL_CAVPO R..EPDSNVI VVDWLRRAQH HYPESADYTK LVGEDVARFI NWMEDEFKYS +LIPL_CHICK R..EPDSNVI VVDWLVRAQQ HYPVSAAYTK LVGKDVAMFI DWMEEKFNYP +LIPL_HUMAN R..EPDSNVI VVDWLSRAQE HYPVSAGYTK LVGQDVARFI NWMEEEFNYP +LIPL_MOUSE R..EPDSNVI VVDWLYRAQQ HYPVSAGYTK LVGNDVARFI NWMEEEFNYP +LIPL_RAT R..EPDSNVI VVDWLYRAQQ HYPVSAGYTK LVGNDVARFI NWLEEEFNYP +LIPP_HORSE V...ESVNCI CVDWKSGSRT AYSQASQNVR IVGAEVAYLV GVLQSSFDYS +LIPP_HUMAN V...ESVNCI CVDWKGGSRT GYTQASQNIR IVGAEVAYFV EFLQSAFGYS +LIPP_PIG V...ESVNCI CVDWKGGSRT GYTQASQNIR IVGAEVAYFV EVLKSSLGYS +LIPP_RABIT V...ETVNCI CVDWKGGSRT TYPQATQNIR IVGAEVAYLV GTLQSSLGYS +LIPP_RAT V...ESVNCI CVDWKGGSRA TYTQATQNVR VVGAEVALLV NVLKSDLGHP + + +LIP1_CANFA PSQVQLIGHS LGAHVAGEAG SRTPG...LG RITGLDPVEA SFQGTPEEVR +LIP2_MOUSE PENVHLIPHS LGSHVAGEAG RRLEGH..VG RITGLDPAEP CFQGLPEEVR +LIPH_HUMAN RSHVHLIGYS LGAHVSGFAG SSIGGTHKIG RITGLDAAGP LFEGSAPSNR +LIPH_MOUSE RSKVHLIGYS LGAHVSGFAG SSMDGKNKIG RITGLDPAGP MFEGTSPNER +LIPH_RAT RSKVHLIGYS LGAHVSGFAG SSMGGKRKIG RITGLDPAGP MFEGTSPNER +LIPL_BOVIN LGNVHLLGYS LGAHAAGIAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR +LIPL_CAVPO VDNVHLLGYS LGAHAAGVAG SRTN..TKVS RITGLDPAGP NFEYAEATSR +LIPL_CHICK LNNVHLLGYS LGAHAAGIAG SLTK..KKVN RITGLDPAGP TFEYADAPIR +LIPL_HUMAN LDNVHLLGYS LGAHAAGIAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR +LIPL_MOUSE LDNVHLLGYS LGAHAAGVAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR +LIPL_RAT LDNVHLLGYS LGAHAAGVAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR +LIPP_HORSE PSNVHIIGHS LGSHAAGEAG RRTNGA..VG RITGLDPAEP CFQGTPELVR +LIPP_HUMAN PSNVHVIGHS LGAHAAGEAG RRTNGT..IG RITGLDPAEP CFQGTPELVR +LIPP_PIG PSNVHVIGHS LGSHAAGEAG RRTNGT..IE RITGLDPAEP CFQGTPELVR +LIPP_RABIT PSNIHVIGHS LGAHAAGEVG RRTNGT..IG RITGLDPAEP YFQGTPEIVR +LIPP_RAT PDNVHLIGHS LGSHVAGEAG KRTFGA..IG RITGLDAAEP YFQGTPEEVR + + +LIP1_CANFA LDPTDADFVD VIHTDAAPLI PFLGFGTSQQ MGHLDFFPNG GEEMPGCKKN +LIP2_MOUSE LDPSDAMFVD VIHTDSAPII PYLGFGMSQK VGHLDFFPNG GKEIPGCQKN +LIPH_HUMAN LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IGHYDFYPNG GSFQPGCHFL +LIPH_MOUSE LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IAHYDFYPNG GSFQPGCHFL +LIPH_RAT LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IAHYDFYPNG GSFQPGCHFL +LIPL_BOVIN LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG +LIPL_CAVPO LSPDDAQFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GSFQPGCNIQ +LIPL_CHICK LSPDDADFVD VLHTYTR.GS PDRSIGIQKP VGHIDIYPNG GGFQPGCNLG +LIPL_HUMAN LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG +LIPL_MOUSE LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG +LIPL_RAT LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG +LIPP_HORSE LDPSDAQFVD VIHTDIAPFI PNLGFGMSQT AGHLDFFPNG GKEMPGCQKN +LIPP_HUMAN LDPSDAKFVD VIHTDGAPIV PNLGFGMSQV VGHLDFFPNG GVEMPGCKKN +LIPP_PIG LDPSDAKFVD VIHTDAAPII PNLGFGMSQT VGHLDFFPNG GKQMPGCQKN +LIPP_RABIT LDPSDAQFVD VIHTDAAPMV PNLGFGMSQT VGHLDFFPNG GKEMPGCQKN +LIPP_RAT LDPTDAQFVD AIHTDAAPII PNLGFGMSQT VGHLDFFPNG GMEMPGCQKN + + +LIP1_CANFA ALSQIVDLDG IWEGTRDFVA CNHLRSYKYY SESILNPDG. FASYPCASYR +LIP2_MOUSE ILSTIVDING IWEGTRNFAA CNHLRSYKYY ASSILNPDG. FLGYPCSSYE +LIPH_HUMAN ELYRHIAQHG FNAITQ.TIK CSHERSVHLF IDSLLHAGTQ SMAYPCGDMN +LIPH_MOUSE ELYKHIAEHG LNAITQ.TIK CAHERSVHPF IDSLQHSDLQ SIGFQCSDMG +LIPH_RAT ELYKHIAEHG LNAITQ.TIN CAHERSVHLF IDSLQHSNLQ NTGFQCSNMD +LIPL_BOVIN EALRVIAERG LGDVDQ.LVK CSHERSVHLF IDSLLNEENP SKAYRCNSKE +LIPL_CAVPO DALRVISQKG FGDMDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE +LIPL_CHICK EALRLIAEKG FSDVDQ.LVK CSHERSIHLF IDSLLYEEKP SMAYRCNTKE +LIPL_HUMAN EAIRVIAERG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCSSKE +LIPL_MOUSE EAIRVIAERG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE +LIPL_RAT EAIRVIAEKG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE +LIPP_HORSE VLSQIVDIDG IWQGTRDFAA CNHLRSYKYY TDSILNPDG. FAGFSCASYS +LIPP_HUMAN ILSQIVDIDG IWEGTRDFAA CNHLRSYKYY TDSIVNPDG. FAGFPCASYN +LIPP_PIG ILSQIVDIDG IWEGTRDFVA CNHLRSYKYY ADSILNPDG. FAGFPCDSYN +LIPP_RABIT VLSQIVDING VWEGTRDFVA CNHLRSYKYY ADSIVNPNG. FAGFSCASYT +LIPP_RAT ILSQIVDIDG IWEGTRDFAA CNHLRSYKYY TDSIVNPTG. FSGFSCSSYN + + +LIP1_CANFA AFESNKCFPC PDQGCPQMGH YADKFAVKTS DETQKYFLNT GDSSNFARWR +LIP2_MOUSE KFQHNDCFPS PEQGCPKMGH YADQFEGKTA TVEQTFFLNT ADTGNFTRWR +LIPH_HUMAN SFSQGLCLSC KKGRCNTLGY HVRQEPRSKS ...KRLFLVT RAQSPFKVYH +LIPH_MOUSE SFSQGLCLSC KKGRCNTLGY DIRKDRSGKS ...KRLFLIT RAQSPFKVYH +LIPH_RAT SFSQGLCLNC KKGRCNSLGY DIRRIGHVKS ...KTLFLIT RAQSPFKVYH +LIPL_BOVIN AFEKGLCLSC RKNRCNNMGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH +LIPL_CAVPO AFEKGLCLSC RKNRCNNVGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH +LIPL_CHICK AFEKGLCLSC RKNRCNNLGY KVNRVRTKRN ...TKMYLKT RAQMPYKVFH +LIPL_HUMAN AFEKGLCLSC RKNRCNNLGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH +LIPL_MOUSE AFEKGLCLSC RKNRCNNLGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH +LIPL_RAT AFEKGLCLSC RKNRCNNVGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH +LIPP_HORSE DFTANKCFPC SSEGCPQMGH YADRFPGRTK GVGQLFYLNT GDASNFARWR +LIPP_HUMAN VFTANKCFPC PSGGCPQMGH YADRYPGKTN DVGQKFYLDT GDASNFARWR +LIPP_PIG VFTANKCFPC PSEGCPQMGH YADRFPGKTN GVSQVFYLNT GDASNFARWR +LIPP_RABIT AFSANKCFPC SN.GCPQMGH YADRFSRKTD GVGQTFYLNT GDSSNFARWR +LIPP_RAT VFSANKCFPC GSEGCPQMGH YADKYPGKTK ELYQKFYLNT GDKSNFARWR + + +LIP1_CANFA YGVSITLSG. ..KR.ATGQA KVALFGSKGN THQFNIFKGI .LKPGSTHSN +LIP2_MOUSE YKVSVTLSGP ..KK.LSGYI LVALYGCNAN SKQYEVFKGS .LQPEARYIR +LIPH_HUMAN YQLKIQFINQ TETP.IQTTF TMSLLGTKEK MQKIPITLGK GIASNKTYSF +LIPH_MOUSE YQFKIQFINQ IEKP.VEPTF TMSLLGTKEE IKRIPITLGE GITSNKTYSF +LIPH_RAT YQFKIQFINQ MEKP.MEPTF TMTLLGTKEE IKKIPITLGE GITSNKTYSL +LIPL_BOVIN YQVKIHFSGT ESNTYTNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF +LIPL_CAVPO YQVKIYFSGT ETTTYTNQAF EISLYGTVAE SENIPFTLPE .VSANNTYSF +LIPL_CHICK YQVKIHFFGK TNVTKVDQPF LISLYGTLDE SENIPFTLPE .VSSNKTFSF +LIPL_HUMAN YQVKIHFSGT ESETHTNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF +LIPL_MOUSE YQVKIHFSGT ENGKQHNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF +LIPL_RAT YQVKIHFSGT ENDKQNNQAF EISLYGTVAE SENIPFTLPE .VATNKTYSF +LIPP_HORSE YRVDVTLSG. ..KK.VTGHV LVSLFGNKGN SRQYEIFQGT .LKPDNTYSN +LIPP_HUMAN YKVSVTLSG. ..KK.VTGHI LVSLFGNKGN SKQYEIFKGT .LKPDSTHSN +LIPP_PIG YKVSVTLSG. ..KK.VTGHI LVSLFGNEGN SRQYEIYKGT .LQPDNTHSD +LIPP_RABIT YQVAVTLSG. ..RR.VTGHV LVSLYGSKGN SKQYEIFTGL .LKPGDTHLN +LIPP_RAT YQVTVTLSG. ..QK.VTGHI LVSLFGNGGN SKQYEVFKGS .LHPGDTHVK + + +LIP1_CANFA EFDAKLDVGT IEKVKFLWNN N..VVNPTFP KVG....... ........AA +LIP2_MOUSE DIDVDVNVGE IQKVKFLWNN K..VINLFRP TMG....... ........AS +LIPH_HUMAN LITLDVDIGE LIMIKFKWEN S..AVWANVW DTVQTIIPWS TGPRHSGLVL +LIPH_MOUSE LITLDKDIGE LILLKFKWEN S..AVWANVW NTVQTIMLWG IEPHHSGLIL +LIPH_RAT LITLNKDIGE LIMLKFKWEN S..AVWANVW NTVQTIMLWD TEPHYAGLIV +LIPL_BOVIN LLYTEVDIGE LLMLKLKWIS DSYFSWSNWW SSP....... ......GFDI +LIPL_CAVPO LIYTEVDIGE LLMLKLKWIT ESYFSWSSWW GRP....... ......TFTI +LIPL_CHICK LIYTEVDIGD LLMLKLQWEK DTFFSWSDWW TPF....... ......AFTI +LIPL_HUMAN LIYTEVDIGE LLMLKLKWKS DSYFSWSDWW SSP....... ......GFAI +LIPL_MOUSE LIYTEVDIGE LLMMKLKWMS DSYFSWPDWW SSP....... ......SFVI +LIPL_RAT LIYTEVDIGE LLMMKLKWKN DSYFRWSDWW SSP....... ......SFVI +LIPP_HORSE EFDSDVEVGD LEKVKFIWYN N..VINLTLP KVG....... ........AS +LIPP_HUMAN EFDSDVDVGD LQMVKFIWYN N..VINPTLP RVG....... ........AS +LIPP_PIG EFDSDVEVGD LQKVKFIWYN NN.VINPTLP RVG....... ........AS +LIPP_RABIT EFDSDVDVGD VQKVKFVWYN N..VINPTLP KVG....... ........AS +LIPP_RAT EFDSDMDVGD LQKVKFIWYN N..VINPTLP KVG....... ........AS + + +LIP1_CANFA KITVQK.GEE KTVHSFCSES TVR....EDV LLTLTPC +LIP2_MOUSE QITLQR.AKD GKEFNFCTSN TVH....EDV LQSLYPC +LIPH_HUMAN KTIRVKAGET QQRMTFCSEN TDDLLLRPTQ EKIFVKC +LIPH_MOUSE KTIWVKAGET QQRMTFCPEN LDDLQLHPSQ EKVFVNC +LIPH_RAT KTIWVKAGET QQRMTFCPDN VDDLQLHPTQ EKVFVKC +LIPL_BOVIN GKIRVKAGET QKKVIFCSRE KMSYLQKGKS PVIFVKC +LIPL_CAVPO EKIRVKAGET QKKIVFCSRE KVSKLQKGKE APVFVKC +LIPL_CHICK QRVRVKSGET QKKVVFCSRD GSSRLGKGEE AAIFVKC +LIPL_HUMAN QKIRVKAGET QKKVIFCSRE KVSHLQKGKA PAVFVKC +LIPL_MOUSE ERIRVKAGET QKKVIFCARE KVSHLQKGKD SAVFVKC +LIPL_RAT EKIRVKAGET QKKVIFCARE KVSHLQKGKD AAVFVKC +LIPP_HORSE KITVER.NDG .SVFNFCSEE TVR....EDV LLTLTAC +LIPP_HUMAN KIIVET.NVG .KQFNFCSPE TVR....EEV LLTLTPC +LIPP_PIG KITVER.NDG .KVYDFCSQE TVR....EEV LLTLNPC +LIPP_RABIT QITVEQ.NDG .RVFKFCSTD TVR....EDI LLTLTPC +LIPP_RAT RISVER.NDG .RVFNFCSQD TVR....EDV LLTLSAC + + diff --git a/website/version2/examples/muscle.jpg b/website/version2/examples/muscle.jpg new file mode 100755 index 0000000..5f89239 Binary files /dev/null and b/website/version2/examples/muscle.jpg differ diff --git a/website/version2/examples/overview.gif b/website/version2/examples/overview.gif new file mode 100755 index 0000000..e961650 Binary files /dev/null and b/website/version2/examples/overview.gif differ diff --git a/website/version2/examples/pca.gif b/website/version2/examples/pca.gif new file mode 100755 index 0000000..6192c3b Binary files /dev/null and b/website/version2/examples/pca.gif differ diff --git a/website/version2/examples/pdb.gif b/website/version2/examples/pdb.gif new file mode 100755 index 0000000..7e1e739 Binary files /dev/null and b/website/version2/examples/pdb.gif differ diff --git a/website/version2/examples/search.gif b/website/version2/examples/search.gif new file mode 100755 index 0000000..4d98c44 Binary files /dev/null and b/website/version2/examples/search.gif differ diff --git a/website/version2/examples/serprot.msf b/website/version2/examples/serprot.msf new file mode 100755 index 0000000..cc5b9b4 --- /dev/null +++ b/website/version2/examples/serprot.msf @@ -0,0 +1,65 @@ +PileUp + + + + MSF: 279 Type: P Check: 9995 .. + + Name: KYBOA oo Len: 279 Check: 4492 Weight: 1.00 + Name: TRBOTR oo Len: 279 Check: 6670 Weight: 1.00 + Name: ELPG oo Len: 279 Check: 6037 Weight: 1.00 + Name: PRRTG oo Len: 279 Check: 3057 Weight: 1.00 + Name: KQHUP oo Len: 279 Check: 6499 Weight: 1.00 + Name: TRSMG oo Len: 279 Check: 3240 Weight: 1.00 + +// + + + +KYBOA .CGVP..... AIQPVLSGLS .........R IVNGEEAVPG SWPWQVSLQD +TRBOTR .......... .....VDDDD .........K IVGGYTCGAN TVPYQVSLN. +ELPG .......... .......... .......... VVGGTEAQRN SWPSQISLQY +PRRTG .......... .......... .......... IIGGVESIPH SRPYMAHLDI +KQHUP AYGTQGSSGY SLRLCNTGDN SVCTTKTSTR IVGGTNSSWG EWPWQVSLQV +TRSMG .......... .......... .......... VVGGTRAAQG EFPFMVRLS. + + +KYBOA K...TGFHFC GGSLINENWV VTAAHCG... ..VTTSDVVV AGEFDQGSSS +TRBOTR ....SGYHFC GGSLINSQWV VSAAHCY... ..KSGIQVRL G.EDNINVVE +ELPG RSGSSWAHTC GGTLIRQNWV MTAAHCVD.. .RELTFRVVV G.EHNLNQNN +PRRTG VTEKGLRVIC GGFLISRQFV LTAAHCK... ..GREITVIL G.AHDVRKRE +KQHUP K.LTAQRHLC GGSLIGHQWV LTAAHCFDGL PLQDVWRIYS G.ILNLSDIT +TRSMG .......MGC GGALYAQDIV LTAAHCVS.. ..GSGNNTSI TATGGVVDLQ + + +KYBOA EKIQKLKIAK VFKNSKYNSL TINN..DITL LKLSTAASFS QTVSAVCLPS +TRBOTR GNEQFISASK SIVHPSYNSN TLNN..DIML IKLKSAASLN SRVASISLPT +ELPG GTEQYVGVQK IVVHPYWNTD DVAAGYDIAL LRLAQSVTLN SYVQLGVLPR +PRRTG STQQKIKVEK QIIHESYNSV PNLH..DIML LKLEKKVELT PAVNVVPLPS +KQHUP KDTPFSQIKE IIIHQNYKVS EGNH..DIAL IKLQAPLNYT EFQKPICLPS +TRSMG S.AVKVRSTK VLQAPGYNGT G.K...DWAL IKLAQPINQ. P.....TLKI + + +KYBOA ASDDFAAGTT CVTTGWGLTR YTNANTPDRL QQASLPLLSN TNCKK..YWG +TRBOTR S..CASAGTQ CLISGWGNTK SSGTSYPDVL KCLKAPILSD SSCKS..AYP +ELPG AGTILANNSP CYITGWGLTR .TNGQLAQTL QQAYLPTVDY AICSSSSYWG +PRRTG PSDFIHPGAM CWAAGWGKTG .VRDPTSYTL REVELRIMDE KACVD...YR +KQHUP KGDTSTIYTN CWVTGWGFSK .EKGEIQNIL QKVNIPLVTN EECQKR.YQD +TRSMG ATTTAYNQGT FTVAGWGANR .EGGSQQRYL LKANVPFVSD AACRS.AYGN + + +KYBOA TKIKDAMICA G...ASGVSS .CMGDSGGPL VCKK.NGAWT LVGIVSWGS. +TRBOTR GQITSNMFCA GY.LEGGKDS .CQGDSGGPV VCS...G..K LQGIVSWGS. +ELPG STVKNSMVCA G...GNGVRS GCQGDSGGPL HCLV.NGQYA VHGVTSFVSR +PRRTG YYEYKFQVCV G..SPTTLRA AFMGDSGGPL LCA...G..V AHGIVSYGH. +KQHUP YKITQRMVCA GY.KEGGKDA .CKGDSGGPL VCKH.NGMWR LVGITSWGE. +TRSMG ELVANEEICA GYPDTGGVDT .CQGDSGGPM FRKDNADEWI QVGIVSWGY. + + +KYBOA .STCSTSTPG VYARVTALVN WVQQTLAAN +TRBOTR .GCAQKNKPG VYTKVCNYVS WIKQTIASN +ELPG LGCNVTRKPT VFTRVSAYIS WINNVIASN +PRRTG ...PDAKPPA IFTRVSTYVP TINAVIN.. +KQHUP .GCARREQPG V......... ......... +TRSMG .GCARPGYPG VYTEVSTFAS AIASAARTL + + diff --git a/website/version2/examples/tree.gif b/website/version2/examples/tree.gif new file mode 100755 index 0000000..e4619dd Binary files /dev/null and b/website/version2/examples/tree.gif differ diff --git a/website/version2/examples/uniprot.gif b/website/version2/examples/uniprot.gif new file mode 100755 index 0000000..a643904 Binary files /dev/null and b/website/version2/examples/uniprot.gif differ diff --git a/website/version2/examples/wrap.gif b/website/version2/examples/wrap.gif new file mode 100755 index 0000000..b67a78b Binary files /dev/null and b/website/version2/examples/wrap.gif differ diff --git a/website/version2/index.html b/website/version2/index.html new file mode 100755 index 0000000..8acf398 --- /dev/null +++ b/website/version2/index.html @@ -0,0 +1,100 @@ + + + + +JalView - Java alignment editor + + + + + + + +
+ + + + +
+ + + + + +
Jalview +
+
a + multiple alignment editor
+
+
+ + + + + +

Downloads

+ + Examples + Reference + Source Code
    +
  • Jalview 2
    • +
+

Feedback

+

   

+


+ +

+

Key features of Jalview Version 2: +

+

Current development allows the Jalview Application to be distributed + using Java Web Start which is installed with Java. + Each time the application is started via Java Web Start an automatic + update is performed so that you will always be running the latest code.
+
+ N.B. if you have a local installation of Java and clicking on the link + below prompts the question "Open using application...", locate + your installation of Java Web Start - its called "javaws". Your web browser will now associate .jnlp + files with Java Web Start
+
+ Try it now. +

+

Start + Jalview

+

 

+
+ If you are having difficulties installing Java or would prefer not to + use Java Web Start you could try installing Jalview from the following + link. +

+

+

Install with InstallAnywhere +

+
+ +
+
+ + diff --git a/website/version2/webstart/JalviewX.jar b/website/version2/webstart/JalviewX.jar new file mode 100755 index 0000000..96d4a5c Binary files /dev/null and b/website/version2/webstart/JalviewX.jar differ diff --git a/website/version2/webstart/JalviewX.jnlp b/website/version2/webstart/JalviewX.jnlp new file mode 100755 index 0000000..16c4b60 --- /dev/null +++ b/website/version2/webstart/JalviewX.jnlp @@ -0,0 +1,43 @@ + + + + Jalview + The Barton Group + + Jalview Multiple Alignment Editor + Jalview + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/website/version2/webstart/activation.jar b/website/version2/webstart/activation.jar new file mode 100755 index 0000000..2cd585b Binary files /dev/null and b/website/version2/webstart/activation.jar differ diff --git a/website/version2/webstart/axis.jar b/website/version2/webstart/axis.jar new file mode 100755 index 0000000..a6ee5e9 Binary files /dev/null and b/website/version2/webstart/axis.jar differ diff --git a/website/version2/webstart/castor.zip b/website/version2/webstart/castor.zip new file mode 100755 index 0000000..1ad484f Binary files /dev/null and b/website/version2/webstart/castor.zip differ diff --git a/website/version2/webstart/commons-discovery.jar b/website/version2/webstart/commons-discovery.jar new file mode 100755 index 0000000..f9fddd8 Binary files /dev/null and b/website/version2/webstart/commons-discovery.jar differ diff --git a/website/version2/webstart/commons-logging.jar b/website/version2/webstart/commons-logging.jar new file mode 100755 index 0000000..281ab3f Binary files /dev/null and b/website/version2/webstart/commons-logging.jar differ diff --git a/website/version2/webstart/jaxrpc.jar b/website/version2/webstart/jaxrpc.jar new file mode 100755 index 0000000..197e6c7 Binary files /dev/null and b/website/version2/webstart/jaxrpc.jar differ diff --git a/website/version2/webstart/jhall.jar b/website/version2/webstart/jhall.jar new file mode 100755 index 0000000..a6231df Binary files /dev/null and b/website/version2/webstart/jhall.jar differ diff --git a/website/version2/webstart/log4j-1.2.8.jar b/website/version2/webstart/log4j-1.2.8.jar new file mode 100755 index 0000000..90b3b11 Binary files /dev/null and b/website/version2/webstart/log4j-1.2.8.jar differ diff --git a/website/version2/webstart/logo_big.gif b/website/version2/webstart/logo_big.gif new file mode 100755 index 0000000..e898c94 Binary files /dev/null and b/website/version2/webstart/logo_big.gif differ diff --git a/website/version2/webstart/mail.jar b/website/version2/webstart/mail.jar new file mode 100755 index 0000000..b8981f5 Binary files /dev/null and b/website/version2/webstart/mail.jar differ diff --git a/website/version2/webstart/regex.jar b/website/version2/webstart/regex.jar new file mode 100755 index 0000000..a73a070 Binary files /dev/null and b/website/version2/webstart/regex.jar differ diff --git a/website/version2/webstart/saaj.jar b/website/version2/webstart/saaj.jar new file mode 100755 index 0000000..39c4276 Binary files /dev/null and b/website/version2/webstart/saaj.jar differ diff --git a/website/version2/webstart/wsdl4j.jar b/website/version2/webstart/wsdl4j.jar new file mode 100755 index 0000000..746f425 Binary files /dev/null and b/website/version2/webstart/wsdl4j.jar differ diff --git a/website/version2/webstart/xercesImpl.jar b/website/version2/webstart/xercesImpl.jar new file mode 100755 index 0000000..5a38fa5 Binary files /dev/null and b/website/version2/webstart/xercesImpl.jar differ diff --git a/website/version2/webstart/xml-apis.jar b/website/version2/webstart/xml-apis.jar new file mode 100755 index 0000000..1c09615 Binary files /dev/null and b/website/version2/webstart/xml-apis.jar differ