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+<!DOCTYPE helpset PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp HelpSet Version 1.0//EN" "http://java.sun.com/products/javahelp/helpset_1_0.dtd">\r
+<helpset version="1.0">\r
+ <!-- title -->\r
+ <title>Jalview Documentation</title>\r
+ <!-- maps -->\r
+ <maps>\r
+ <homeID>home</homeID>\r
+ <mapref location="help.jhm" />\r
+ </maps>\r
+ <!-- views -->\r
+ <view>\r
+ <name>TOC</name>\r
+ <label>Table Of Contents</label>\r
+ <type>javax.help.TOCView</type>\r
+ <data>helpTOC.xml</data>\r
+ </view>\r
+ <view>\r
+ <name>Index</name>\r
+ <label>Index</label>\r
+ <type>javax.help.IndexView</type>\r
+ <data>helpIndex.xml</data>\r
+ </view>\r
+ <view>\r
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+ <label>Search</label>\r
+ <type>javax.help.SearchView</type>\r
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+</helpset>\r
--- /dev/null
+<?xml version="1.0" encoding="ISO-8859-1" ?>\r
+ <!DOCTYPE map PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Map Version 1.0//EN" "http://java.sun.com/products/javahelp/map_1_0.dtd">\r
+<map version="1.0">\r
+ <mapID target="home" url="html/index.html" />\r
+ \r
+ <mapID target="calculate" url="html/menus/calculateMenu.html" />\r
+ \r
+ <mapID target="colours" url="html/colourSchemes/colourSchemes.html" />\r
+ <mapID target="colours.zappo" url="html/colourSchemes/colourSchemes.html#zappo" />\r
+ <mapID target="colours.taylor" url="html/colourSchemes/colourSchemes.html#taylor" />\r
+ <mapID target="colours.hydro" url="html/colourSchemes/colourSchemes.html#hydrophobic" />\r
+ <mapID target="colours.helix" url="html/colourSchemes/colourSchemes.html#helix" />\r
+ <mapID target="colours.strand" url="html/colourSchemes/colourSchemes.html#strand" />\r
+ <mapID target="colours.turn" url="html/colourSchemes/colourSchemes.html#turn" />\r
+ <mapID target="colours.buried" url="html/colourSchemes/colourSchemes.html#buried" />\r
+ <mapID target="colours.nucleotide" url="html/colourSchemes/colourSchemes.html#nucleotide" />\r
+ <mapID target="colours.blosum" url="html/colourSchemes/colourSchemes.html#blosum" />\r
+ <mapID target="colours.pid" url="html/colourSchemes/colourSchemes.html#pid" />\r
+ \r
+ <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />\r
+ <mapID target="geneticCode" url="html/misc/geneticCode.html" />\r
+ \r
+</map>\r
--- /dev/null
+<?xml version="1.0" encoding="ISO-8859-1" ?>\r
+<!DOCTYPE index PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Index Version 1.0//EN" "http://java.sun.com/products/javahelp/index_1_0.dtd">\r
+<index version="1.0">\r
+ <indexitem text="Menus">\r
+ <indexitem text="File" target="home"/>\r
+ <indexitem text="Edit" target="home"/>\r
+ <indexitem text="Font" target="home"/>\r
+ <indexitem text="View" target="home"/>\r
+ <indexitem text="Colour" target="home"/>\r
+ <indexitem text="Calculate" target="home"/>\r
+ <indexitem text="Align" target="home"/>\r
+ </indexitem>\r
+</index>\r
--- /dev/null
+<?xml version="1.0" encoding="ISO-8859-1" ?>\r
+<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">\r
+<toc version="1.0">\r
+<tocitem text="Menus" expand="true" >\r
+ <tocitem text="File" target="home"/>\r
+ <tocitem text="Edit" target="home"/>\r
+ <tocitem text="Font" target="home"/>\r
+ <tocitem text="View" target="home"/>\r
+ <tocitem text="Colour" target="colours">\r
+ <tocitem text="Zappo" target="colours.zappo"/>\r
+ <tocitem text="Taylor" target="colours.taylor"/>\r
+ <tocitem text="Hydrophobicity" target="colours.hydro"/>\r
+ <tocitem text="Helix propensity" target="colours.helix"/>\r
+ <tocitem text="Strand propensity" target="colours.strand"/>\r
+ <tocitem text="Turn propensity" target="colours.turn"/>\r
+ <tocitem text="Buried index" target="colours.buried"/>\r
+ <tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
+ <tocitem text="Blosum62" target="colours.blosum"/>\r
+ <tocitem text="PID" target="colours.pid"/> \r
+ </tocitem>\r
+ <tocitem text="Calculate" target="calculate"/>\r
+ <tocitem text="Align" target="home"/>\r
+</tocitem>\r
+<tocitem text="Useful information">\r
+ <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
+ <tocitem text="The Genetic Code" target="geneticCode"/>\r
+</tocitem>\r
+</toc>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
+<html>\r
+<head>\r
+<title>Untitled Document</title>\r
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em><a name="zappo">Zappo Colour</a>s</em><br>\r
+ <br>\r
+ The residues are coloured according to their physico-chemical properties as \r
+ follows: </p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr> \r
+ <td > Aliphatic/hydrophobic</td>\r
+ <td bgcolor="#ffafaf">ILVAM </td>\r
+ </tr>\r
+ <tr> \r
+ <td>Aromatic</td>\r
+ <td bgcolor="#ffc800">FWY</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Positive</td>\r
+ <td bgcolor="#6464ff">KRH</td>\r
+ </tr>\r
+ <tr> \r
+ <td> Negative</td>\r
+ <td bgcolor="#ff0000">DE</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Hydrophilic</td>\r
+ <td bgcolor="#00ff00">STNQ</td>\r
+ </tr>\r
+ <tr> \r
+ <td>conformationally special</td>\r
+ <td bgcolor="#ff00ff">PG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Cysteine</td>\r
+ <td bgcolor="#ffff00">C</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"></p>\r
+<p><em><a name="taylor">Taylor</a></em></p>\r
+<p>These colours were invented by Willie Taylor and an entertaining description \r
+ of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr> \r
+ <td bgcolor="#ccff00">A</td>\r
+ <td bgcolor="#99ff00">V</td>\r
+ <td bgcolor="#66ff00">I</td>\r
+ <td bgcolor="#33ff00">L</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#00ff00">M</td>\r
+ <td bgcolor="#00ff66">F</td>\r
+ <td bgcolor="#00ffcc">Y</td>\r
+ <td bgcolor="#00ccff">W</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#0066ff">H</td>\r
+ <td bgcolor="#0000ff">R</td>\r
+ <td bgcolor="#6600ff">K</td>\r
+ <td bgcolor="#cc00ff">N</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#ff00cc">Q</td>\r
+ <td bgcolor="#ff0066">E</td>\r
+ <td bgcolor="#ff0000">D</td>\r
+ <td bgcolor="#ff3300">S</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#ff6600">T</td>\r
+ <td bgcolor="#ff9900">G</td>\r
+ <td bgcolor="#ffcc00">P</td>\r
+ <td bgcolor="#ffff00">C</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"> </p>\r
+<p><em><a name="hydrophobic">Hydrophobicity</a></em></p>\r
+<p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J. \r
+ Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this \r
+ table are coloured red and the most hydrophilic ones are coloured blue.</p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr> \r
+ <td bgcolor="#ff0000">I</td>\r
+ <td bgcolor="#f60009">V</td>\r
+ <td bgcolor="#ea0015">L</td>\r
+ <td bgcolor="#cb0034">F</td>\r
+ <td bgcolor="#c2003d">C</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#b0004f">M</td>\r
+ <td bgcolor="#ad0052">A</td>\r
+ <td bgcolor="#6a0095">G</td>\r
+ <td bgcolor="#680097">X</td>\r
+ <td bgcolor="#61009e">T</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#5e00a1">S</td>\r
+ <td bgcolor="#5b00a4">W</td>\r
+ <td bgcolor="#4f00b0">Y</td>\r
+ <td bgcolor="#4600b9">P</td>\r
+ <td bgcolor="#1500ea">H</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#0c00f3">E</td>\r
+ <td bgcolor="#0c00f3">Z</td>\r
+ <td bgcolor="#0c00f3">Q</td>\r
+ <td bgcolor="#0c00f3">D</td>\r
+ <td bgcolor="#0c00f3">B</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#0c00f3">N</td>\r
+ <td bgcolor="#0000ff">K</td>\r
+ <td bgcolor="#0000ff">R</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"> </p>\r
+<p><em><a name="helix">Helix Propensity</a></em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr> \r
+ <td bgcolor="#ff00ff">E</td>\r
+ <td bgcolor="#ef10ef">M</td>\r
+ <td bgcolor="#e718e7">A</td>\r
+ <td bgcolor="#c936c9">Z</td>\r
+ <td bgcolor="#ae51ae">L</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#a05fa0">K</td>\r
+ <td bgcolor="#986798">F</td>\r
+ <td bgcolor="#926d92">Q</td>\r
+ <td bgcolor="#8a758a">I</td>\r
+ <td bgcolor="#8a758a">W</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#857a85">V</td>\r
+ <td bgcolor="#778877">D</td>\r
+ <td bgcolor="#758a75">X</td>\r
+ <td bgcolor="#758a75">H</td>\r
+ <td bgcolor="#6f906f">R</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#49b649">B</td>\r
+ <td bgcolor="#47b847">T</td>\r
+ <td bgcolor="#36c936">S</td>\r
+ <td bgcolor="#23dc23">C</td>\r
+ <td bgcolor="#21de21">Y</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#1be41b">N</td>\r
+ <td bgcolor="#00ff00">G</td>\r
+ <td bgcolor="#00ff00">P</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"> </p>\r
+<p><em><a name="strand">Strand propensity</a></em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr> \r
+ <td bgcolor="#ffff00">V</td>\r
+ <td bgcolor="#ecec13">I</td>\r
+ <td bgcolor="#d3d32c">Y</td>\r
+ <td bgcolor="#c2c23d">F</td>\r
+ <td bgcolor="#c0c03f">W</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#b2b24d">L</td>\r
+ <td bgcolor="#9d9d62">T</td>\r
+ <td bgcolor="#9d9d62">C</td>\r
+ <td bgcolor="#8c8c73">Q</td>\r
+ <td bgcolor="#82827d">M</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#797986">X</td>\r
+ <td bgcolor="#6b6b94">R</td>\r
+ <td bgcolor="#64649b">N</td>\r
+ <td bgcolor="#60609f">H</td>\r
+ <td bgcolor="#5858a7">A</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#4949b6">S</td>\r
+ <td bgcolor="#4949b6">G</td>\r
+ <td bgcolor="#4747b8">Z</td>\r
+ <td bgcolor="#4747b8">K</td>\r
+ <td bgcolor="#4343bc">B</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#2323dc">P</td>\r
+ <td bgcolor="#2121de">D</td>\r
+ <td bgcolor="#0000ff">E</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"> </p>\r
+<p><em><a name="turn">Turn propensity</a></em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr> \r
+ <td bgcolor="#ff0000">N</td>\r
+ <td bgcolor="#ff0000">G</td>\r
+ <td bgcolor="#f60909">P</td>\r
+ <td bgcolor="#f30c0c">B</td>\r
+ <td bgcolor="#e81717">D</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#e11e1e">S</td>\r
+ <td bgcolor="#a85757">C</td>\r
+ <td bgcolor="#9d6262">Y</td>\r
+ <td bgcolor="#7e8181">K</td>\r
+ <td bgcolor="#7c8383">X</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#778888">Q</td>\r
+ <td bgcolor="#738c8c">W</td>\r
+ <td bgcolor="#738c8c">T</td>\r
+ <td bgcolor="#708f8f">R</td>\r
+ <td bgcolor="#708f8f">H</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#5ba4a4">Z</td>\r
+ <td bgcolor="#3fc0c0">E</td>\r
+ <td bgcolor="#2cd3d3">A</td>\r
+ <td bgcolor="#1ee1e1">F</td>\r
+ <td bgcolor="#1ee1e1">M</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#1ce3e3">L</td>\r
+ <td bgcolor="#07f8f8">V</td>\r
+ <td bgcolor="#00ffff">I</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"> </p>\r
+<p><em><a name="buried"></a>Buried index</a></em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr> \r
+ <td bgcolor="#0000ff">C</td>\r
+ <td bgcolor="#0054ab">I</td>\r
+ <td bgcolor="#005fa0">V</td>\r
+ <td bgcolor="#007b84">L</td>\r
+ <td bgcolor="#008778">F</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#009768">M</td>\r
+ <td bgcolor="#009d62">G</td>\r
+ <td bgcolor="#00a35c">A</td>\r
+ <td bgcolor="#00a857">W</td>\r
+ <td bgcolor="#00b649">X</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#00d52a">S</td>\r
+ <td bgcolor="#00d52a">H</td>\r
+ <td bgcolor="#00db24">T</td>\r
+ <td bgcolor="#00e01f">P</td>\r
+ <td bgcolor="#00e619">Y</td>\r
+ </tr>\r
+ <tr> \r
+ <td bgcolor="#00eb14">N</td>\r
+ <td bgcolor="#00eb14">B</td>\r
+ <td bgcolor="#00eb14">D</td>\r
+ <td bgcolor="#00f10e">Q</td>\r
+ <td bgcolor="#00f10e">Z</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#00f10e">E</td>\r
+ <td bgcolor="#00fc03">R</td>\r
+ <td bgcolor="#00ff00">K</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"> </p>\r
+<p><em></em><a name="nucleotide">Nucleotide Colours</a></em></p>\r
+<div align="center">\r
+ <table width="200" border="1">\r
+ <tr> \r
+ <td bgcolor="#64F73F">A</td>\r
+ <td bgcolor="#FFB340">C</td>\r
+ <td bgcolor="#EB413C">G</td>\r
+ <td bgcolor="#3C88EE">T</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+<p align="center"> </p>\r
+<p><em><a name="blosum"></a>Blosum62</a></em></p>\r
+<p>Gaps are coloured white. If a residue matchs the consensus sequence residue \r
+ at that position it is colored dark blue. If it does not match the consensus \r
+ residue but the 2 residues have a positive Blosum62 score, it is colored light \r
+ blue.</p>\r
+<p> </p>\r
+<p><em><a name="pid">Colouring above a percentage identity threshold</a></em><br>\r
+ Selecting this option causes the colour scheme to be applied to only those residues \r
+ that occur in that column more than a certain percentage of the time. For instance \r
+ selecting the threshold to be 100 will only colour those columns with 100 % \r
+ identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity \r
+ and User colour schemes. <br>\r
+ This option depends on a consensus calculation having been performed. If no \r
+ consensus exists (e.g. after a copy or a clustalw alignment) then no residues \r
+ are coloured.</p>\r
+<p><em>PID Colours</em><br>\r
+ This depends on the applet having performed a consensus calculation on the alignment.<br>\r
+ The PID option colours the residues (boxes and/or text) according to the percentage \r
+ of the residues in each column that agree with the consensus sequence. Only \r
+ the residues that agree with the consensus residue for each column are coloured.<br>\r
+</p>\r
+<p> </p>\r
+<p> </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
+<html>\r
+<head>\r
+<title>Untitled Document</title>\r
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
+</head>\r
+\r
+<body>\r
+<h1 align="center"><br>\r
+ <img src="images/align.gif" width="200" height="80" align="baseline"> Jalview \r
+ Documentation </h1>\r
+<p align="center">Your guide to Jalview</p>\r
+</body>\r
+</html>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
+<html>\r
+<head>\r
+<title>Untitled Document</title>\r
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
+</head>\r
+\r
+<body>\r
+Calculate menu<br>\r
+Consensus sequence <br>\r
+Sorting sequence by pairwise identity to consensus <br>\r
+Sorting by tree order <br>\r
+Sorting by group order <br>\r
+Removing redundancy of sequences <br>\r
+Smith-Waterman pairwise alignment <br>\r
+Principal component analysis <br>\r
+UPGMA tree using percentage identity distances <br>\r
+Neighbour joining tree using percentage identity distances <br>\r
+Conservation <br>\r
+<br>\r
+Consensus sequence<br>\r
+Each residue in the consensus sequence is the most frequent residue in each column \r
+of the alignment excluding gap residues ' ','-' and '.' . You can't access the \r
+consensus sequence directly but it is used in the PID colour scheme. <br>\r
+When the editor first starts up the consensus sequence is automatically calculated \r
+using all the sequences in the alignment and the PID colour scheme is used as \r
+default. If the consensus option is selected again only the currently selected \r
+sequences are used to calculate it and all sequences in the alignment are coloured \r
+according to that consensus. <br>\r
+<p>Sorting sequences<br>\r
+ Once a consensus calculation has been done selecting this option will sort the \r
+ selected sequences by their percentage identity to the consensus sequence. The \r
+ most similar sequence is put at the top. If no sequences are selected then redundancy \r
+ is removed from the whole alignment. <br>\r
+ Sorting by tree order<br>\r
+ If a UPGMA tree or a neighbour joining tree has been displayed then the main \r
+ alignment window displays the sequences in the same order as they appear in \r
+ the tree. This makes for easier comparison of the tree and the alignment. <br>\r
+ <br>\r
+ Sorting by group order<br>\r
+ If the sequences have been grouped either by hand or by selecting a point on \r
+ the tree then this option will reorder the alignment so all sequences in the \r
+ same group are together. The largest group is shown at the top of the alignment \r
+ and the smallest at the bottom. <br>\r
+ Removing redundancy<br>\r
+ Selecting this option brings up a window asking you to select a threshold. If \r
+ the percentage identity between two sequences exceeds this value one of the \r
+ sequences (the shorter) is discarded. The redundancy calculation is done when \r
+ the Apply button is pressed. For large numbers of sequences this can take a \r
+ long time as all pairs have to be compared. <br>\r
+ Pairwise alignment (Proteins only)<br>\r
+ This calculation is performed on the selected sequences only. Java is not the \r
+ fastest language in the world and aligning more than a handful of sequences \r
+ will take a fair amount of time. <br>\r
+ For each pair of sequences the best global alignment is found using BLOSUM62 \r
+ as the scoring matrix. The scores reported are the raw scores. The sequences \r
+ are aligned using a dynamic programming technique and using the following gap \r
+ penalties : </p>\r
+<p>Gap open : 12 <br>\r
+ Gap extend : 2 </p>\r
+<p>When you select the pairwise alignment option a new window will come up which \r
+ will display the alignments in a text format as they are calculated. Also displayed \r
+ is information about the alignment such as alignment score, length and percentage \r
+ identity between the sequences. </p>\r
+<p>If you want to save that pairwise alignment (it's not in any known format I'm \r
+ afraid) you can cut and paste it from the text window with the mouse. You can \r
+ also press the 'View in alignment editor' button to bring up another editor \r
+ window. <br>\r
+</p>\r
+<p>Principal Component Analysis<br>\r
+ This is a method of clustering sequences based on the method developed by G. \r
+ Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2, February \r
+ 1995 . Extra information can also be found at the SeqSpace server at the EBI. \r
+ <br>\r
+ The version implemented here only looks at the clustering of whole sequences \r
+ and not individual positions in the alignment to help identify functional residues. \r
+ For large alignments plans are afoot to use the CORBA server written by Chris \r
+ Dodge to do this 'residue space' PCA remotely. </p>\r
+<p>When the Calculate->Principal component analysis option is selected all \r
+ the sequences (not just the selected ones) are used in the calculation and for \r
+ large numbers of sequences this could take quite a time. When the calculation \r
+ is finished a new window is displayed showing the projections of the sequences \r
+ along the 2nd, 3rd and 4th vectors giving a 3dimensional view of how the sequences \r
+ cluster. </p>\r
+<p>This 3d view can be rotated by holding the left mouse button down in the PCA \r
+ window and moving it. The user can also zoom in and out by using the up and \r
+ down arrow keys. </p>\r
+<p>Individual points can be selected using the mouse and selected sequences show \r
+ up green in the PCA window and the usual grey background/white text in the alignment \r
+ and tree windows. </p>\r
+<p>Different eigenvectors can be used to do the projection by changing the selected \r
+ dimensions in the 3 menus underneath the 3d window. <br>\r
+</p>\r
+<p>UPGMA tree<br>\r
+ If this option is selected from the Calculate menu then all sequences are used \r
+ to generate a UPGMA tree. The pairwise distances used to cluster the sequences \r
+ are the percentage mismatch between two sequences. For a reliable phylogenetic \r
+ tree I recommend other programs (phylowin, phylip) should be used as they have \r
+ the speed to use better distance methods and bootstrapping. Again, plans are \r
+ afoot for a server to do this and to be able to read in tree files generated \r
+ by other programs. <br>\r
+ When the tree has been calculated a new window is displayed showing the tree \r
+ with labels on the leaves showing the sequence ids. The user can select the \r
+ ids with the mouse and the selected sequences will also be selected in the alignment \r
+ window and the PCA window if that analysis has been calculated. </p>\r
+<p>Selecting the 'show distances' checkbox will put branch lengths on the branches. \r
+ These branch lengths are the percentage mismatch between two nodes. </p>\r
+<p>Postscript output can be generated for this tree and mailed to you by clicking \r
+ the Output button. This will bring up a window asking you for your email address \r
+ and you can set font options and the page orientation. Clicking the Apply button \r
+ will generate the postscript and send the email. <br>\r
+</p>\r
+<p>Neighbour Joining tree<br>\r
+ The distances between sequences for this tree are generated in the same way \r
+ as for the UPGMA tree. The method of clustering is the neighbour joining method \r
+ which doesn't just pick the two closest leaves to cluster together but compensates \r
+ for long edges by subtracting from the distances the average distance from each \r
+ leaf to all the others. <br>\r
+ Selection and output options are the same as for the UPGMA tree.</p>\r
+<p> Conservation<br>\r
+ This option is based on the AMAS method of multiple sequence alignment analysis \r
+ (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
+ for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). \r
+ <br>\r
+ Hierarchical analysis is based on each residue having certain physico-chemical \r
+ properties listed as follows: <br>\r
+ <br>\r
+ <br>\r
+ <br>\r
+</p>\r
+<p>In brief go about it like this : <br>\r
+</p>\r
+<p>The alignment can first be divided into groups. This is best done by first \r
+ creating an average distance tree (Calculate->Average distance tree). Selecting \r
+ a position on the tree will cluster the sequences into groups depending on the \r
+ position selected. Each group is coloured a different colour which is used for \r
+ both the ids in the tree and alignment windows and the sequences themselves. \r
+ If a PCA window is visible a visual comparison can be made between the clustering \r
+ based on the tree and the PCA. <br>\r
+ This link provides an example of the output after grouping for Pfam family rnaseH: \r
+</p>\r
+<p>The grouping by tree may not be satisfactory and the user may want to edit \r
+ the groups (Edit->Groups...) to put any outliers together. </p>\r
+<p>Before selecting the conservation option change the colour scheme to something \r
+ sensible (Taylor or hydrophobicity for example). When the conservation is done \r
+ the existing colour scheme is modified so that the most conserved columns in \r
+ each group have the most intense colours and the least conserved are the palest. \r
+</p>\r
+<p> </p>\r
+<p>This link shows the results of first colouring the alignment by hydrophobicity \r
+ (Colour->by hydrophobicity) then performing conservation analysis (Calculate->Conservation). \r
+ Conserved hydrophobic columns are shown with predominately red residues and \r
+ conserved hydrophilic columns with blue. The most conserved regions have the \r
+ brightest colours. <br>\r
+</p>\r
+<p> <br>\r
+ <br>\r
+ Here is shown the same conservation but with Taylor colours instead of hydrophobicity \r
+ (Colour->Taylor). <br>\r
+</p>\r
+<p>The conservation analysis is done on each sequence group. This highlights differences \r
+ and similarities in conserved residue properties between groups. </p>\r
+<p></p>\r
+</body>\r
+</html>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
+<html>\r
+<head>\r
+<title>Untitled Document</title>\r
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+ background-color: FFFFEE;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+\r
+\r
+<div align="center">\r
+ <h2><br>\r
+ </h2>\r
+ <table WIDTH="441" BORDER cellpadding="3" BGCOLOR="#FFFFFF">\r
+ <tr> \r
+ <td width="15">A</td>\r
+ <td width="25">Ala</td>\r
+ <td width="157">Alanine</td>\r
+ <td width="192">GCT, GCC, GCA, GCG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>B</td>\r
+ <td> </td>\r
+ <td>either aspartic acid or asparagine</td>\r
+ <td> </td>\r
+ </tr>\r
+ <tr> \r
+ <td>C</td>\r
+ <td>Cys</td>\r
+ <td>Cysteine</td>\r
+ <td>TGT, TGC</td>\r
+ </tr>\r
+ <tr> \r
+ <td>D</td>\r
+ <td>Asp</td>\r
+ <td>Aspartic Acid</td>\r
+ <td>GAT, GAC</td>\r
+ </tr>\r
+ <tr> \r
+ <td>E</td>\r
+ <td>Glu</td>\r
+ <td>Glutamic Acid</td>\r
+ <td>GAA, GAG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>F</td>\r
+ <td>Phe</td>\r
+ <td>Phenylalanine</td>\r
+ <td>TTT, TTC</td>\r
+ </tr>\r
+ <tr> \r
+ <td>G</td>\r
+ <td>Gly</td>\r
+ <td>Glycine</td>\r
+ <td>GGT, GGC, GGA, GGG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>H</td>\r
+ <td>His</td>\r
+ <td>Histidine</td>\r
+ <td>CAT, CAC</td>\r
+ </tr>\r
+ <tr> \r
+ <td>I</td>\r
+ <td>Ile</td>\r
+ <td>Isoleucine</td>\r
+ <td>ATT, ATC, ATA</td>\r
+ </tr>\r
+ <tr> \r
+ <td>K</td>\r
+ <td>Lys</td>\r
+ <td>Lysine</td>\r
+ <td>AAA, AAG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>L</td>\r
+ <td>Leu</td>\r
+ <td>Leucine</td>\r
+ <td>TTG, TTA, CTT, CTC, CTA, CTG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>M</td>\r
+ <td>Met</td>\r
+ <td>Methionine</td>\r
+ <td>ATG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>N</td>\r
+ <td>Asn</td>\r
+ <td>Asparagine</td>\r
+ <td>AAT, AAC</td>\r
+ </tr>\r
+ <tr> \r
+ <td>P</td>\r
+ <td>Pro</td>\r
+ <td>Proline</td>\r
+ <td>CCT, CCC, CCA, CCG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Q</td>\r
+ <td>Gln</td>\r
+ <td>Glutamine</td>\r
+ <td>CAA, CAG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>R</td>\r
+ <td>Arg</td>\r
+ <td>Arginine</td>\r
+ <td>CGT, CGC, CGA, CGG, AGA, AGG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>S</td>\r
+ <td>Ser</td>\r
+ <td>Serine</td>\r
+ <td>TCT, TCC, TCA, TCG, AGT, AGC</td>\r
+ </tr>\r
+ <tr> \r
+ <td>T</td>\r
+ <td>Thr</td>\r
+ <td>Threonine</td>\r
+ <td>ACT, ACC, ACA, ACG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>V</td>\r
+ <td>Val</td>\r
+ <td>Valine</td>\r
+ <td>GTT, GTC, GTA, GTG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>W</td>\r
+ <td>Trp</td>\r
+ <td>Tryptophan</td>\r
+ <td>TGG</td>\r
+ </tr>\r
+ <tr> \r
+ <td>X</td>\r
+ <td> </td>\r
+ <td>UNKNOWN</td>\r
+ <td> </td>\r
+ </tr>\r
+ <tr> \r
+ <td>Y</td>\r
+ <td>Tyr</td>\r
+ <td>Tyrosine</td>\r
+ <td>TAT, TAC</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Z</td>\r
+ <td> </td>\r
+ <td>either glutamic acid or glutamine</td>\r
+ <td> </td>\r
+ </tr>\r
+ <tr> \r
+ <td> </td>\r
+ <td>End</td>\r
+ <td>Terminator</td>\r
+ <td>TAA, TAG, TGA</td>\r
+ </tr>\r
+ </table>\r
+ <h2><br>\r
+ </h2>\r
+ </div>\r
+</body>\r
+</html>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
+<html>\r
+<head>\r
+<title>Untitled Document</title>\r
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+\r
+\r
+<div align="center"> \r
+ <h2>The Genetic Code </h2>\r
+ <table border="0">\r
+ <tr> \r
+ <td width="19%"> </td>\r
+ <td width="60%">2nd Position</td>\r
+ <td width="21%"> </td>\r
+ </tr>\r
+ <tr> \r
+ <td><p>1st Position</p>\r
+ <p>(5' end)</p></td>\r
+ <td><table border=5 cellpadding=3>\r
+ <tr align=center bgcolor="#FFFFEE"> \r
+ <td></td>\r
+ <td><h2>U</h2></td>\r
+ <td><h2>C</h2></td>\r
+ <td><h2>A</h2></td>\r
+ <td><h2>G</h2></td>\r
+ <td></td>\r
+ </tr>\r
+ <tr align=center bgcolor="#FFFFEE"> \r
+ <td><h1>U</h1></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Phe</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Phe</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Leu</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Leu</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Ser</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ser</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ser</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ser</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Tyr</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Tyr</td>\r
+ </tr>\r
+ <tr> \r
+ <td>STOP</i></td>\r
+ </tr>\r
+ <tr> \r
+ <td>STOP</i></td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Cys</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Cys</td>\r
+ </tr>\r
+ <tr> \r
+ <td>STOP</i></td>\r
+ </tr>\r
+ <tr> \r
+ <td>Trp</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>U</td>\r
+ </tr>\r
+ <tr> \r
+ <td>C</td>\r
+ </tr>\r
+ <tr> \r
+ <td>A</td>\r
+ </tr>\r
+ <tr> \r
+ <td>G</td>\r
+ </tr>\r
+ </table></td>\r
+ </tr>\r
+ <tr bgcolor="#FFFFEE"> \r
+ <td><h1>C</h1></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Leu</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Leu</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Leu</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Leu</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Pro</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Pro</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Pro</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Pro</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>His</td>\r
+ </tr>\r
+ <tr> \r
+ <td>His</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Gln</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Gln</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Arg</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Arg</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Arg</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Arg</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>U</td>\r
+ </tr>\r
+ <tr> \r
+ <td>C</td>\r
+ </tr>\r
+ <tr> \r
+ <td>A</td>\r
+ </tr>\r
+ <tr> \r
+ <td>G</td>\r
+ </tr>\r
+ </table></td>\r
+ </tr>\r
+ <tr bgcolor="#FFFFEE"> \r
+ <td><h1>A</h1></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Ile</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ile</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ile</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Met</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Thr</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Thr</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Thr</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Thr</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Asn</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Asn</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Lys</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Lys</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Ser</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ser</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Arg</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Arg</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>U</td>\r
+ </tr>\r
+ <tr> \r
+ <td>C</td>\r
+ </tr>\r
+ <tr> \r
+ <td>A</td>\r
+ </tr>\r
+ <tr> \r
+ <td>G</td>\r
+ </tr>\r
+ </table></td>\r
+ </tr>\r
+ <tr bgcolor="#FFFFEE"> \r
+ <td><h1>G</h1></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Val</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Val</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Val</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Val</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Ala</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ala</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ala</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Ala</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Asp</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Asp</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Glu</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Glu</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>Gly</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Gly</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Gly</td>\r
+ </tr>\r
+ <tr> \r
+ <td>Gly</td>\r
+ </tr>\r
+ </table></td>\r
+ <td> <table border=0>\r
+ <tr> \r
+ <td>U</td>\r
+ </tr>\r
+ <tr> \r
+ <td>C</td>\r
+ </tr>\r
+ <tr> \r
+ <td>A</td>\r
+ </tr>\r
+ <tr> \r
+ <td>G</td>\r
+ </tr>\r
+ </table></td>\r
+ </tr>\r
+ </table></td>\r
+ <td><p>3rd Position</p>\r
+ <p>(3'end)</p></td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+#! /bin/sh
+# This builds a search database
+
+# Cygwin support. $cygwin _must_ be set to either true or false.
+case "`uname`" in
+ CYGWIN*) cygwin=true ;;
+ *) cygwin=false ;;
+esac
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin; then
+ [ -n "$JAVAHELP_HOME" ] &&
+ JAVAHELP_HOME=`cygpath --unix "$JAVAHELP_HOME"`
+fi
+
+if [ "$JAVAHELP_HOME" = "" ] ; then
+ # try to find jhindexer
+ if [ -d /opt/javahelp ] ; then
+ JAVAHELP_HOME=/opt/javahelp
+ fi
+
+ if [ -d ${HOME}/opt/jhindexer ] ; then
+ JAVAHELP_HOME=${HOME}/opt/javahelp
+ fi
+
+ ## resolve links - $0 may be a link to javahelp's home
+ PRG=$0
+ progname=`basename $0`
+
+ while [ -h "$PRG" ] ; do
+ ls=`ls -ld "$PRG"`
+ link=`expr "$ls" : '.*-> \(.*\)$'`
+ if expr "$link" : '.*/.*' > /dev/null; then
+ PRG="$link"
+ else
+ PRG="`dirname $PRG`/$link"
+ fi
+ done
+
+ JAVAHELP_HOME=`dirname "$PRG"`/../..
+
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+ JAVAHELP_HOME=`cygpath --path --windows "$JAVAHELP_HOME"`
+fi
+
+java -jar $JAVAHELP_HOME/javahelp/bin/jhindexer.jar "$@"
git://source.jalview.org / jalview.git / commitdiff
