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JPRED-2 Add alscript to the Git repository
[jpred.git] / sources / alscript / doc / alscript / alscript.html
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+<HEAD>
+<TITLE>No Title</TITLE>
+</HEAD>
+<BODY><P>
+ <HR> <A NAME=tex2html1 HREF=tableofcontents3_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/next_motif.gif"></A> <IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/up_motif_gr.gif"> <IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/previous_motif_gr.gif"> <A NAME=tex2html3 HREF=tableofcontents3_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/contents_motif.gif"></A> <BR>
+<B> Next:</B> <A NAME=tex2html2 HREF=tableofcontents3_1.html>Contents</A>
+<HR> <P>
+<P>
+<b>
+<P>
+User Guide to
+<P>
+ALSCRIPT - Sequence alignment to PostScript<BR>Version 2.03<BR></b>
+<P>
+<em>Geoffrey J. Barton</em>
+<P>
+Laboratory of Molecular Biophysics<BR>University of Oxford<BR>Rex Richards Building<BR>South Parks Road<BR>Oxford OX1 3QU<BR>U.K.<BR>
+<P>
+Tel:  (44) 1865-275368<BR>Fax:  (44) 1865-510454<BR>e-mail:  gjb@bioch.ox.ac.uk
+<P>
+REFERENCE:<BR>Barton, G. J. (1993),<BR>ALSCRIPT a tool to format multiple sequence alignments<BR>Protein Engineering, Volume 6, No. 1, pp.37-40.<BR>
+<P>
+<HR>
+<UL> 
+<LI> <A NAME=tex2html4 HREF=tableofcontents3_1.html#SECTION0001000000000000000>Contents</A>
+<LI> <A NAME=tex2html5 HREF=section3_2.html#SECTION0002000000000000000> Update History</A>
+<LI> <A NAME=tex2html6 HREF=section3_3.html#SECTION0003000000000000000> Read This First - VERSION 2.0</A>
+<LI> <A NAME=tex2html7 HREF=section3_4.html#SECTION0004000000000000000> Related Programs</A>
+<LI> <A NAME=tex2html8 HREF=section3_5.html#SECTION0005000000000000000> Availability</A>
+<LI> <A NAME=tex2html9 HREF=section3_6.html#SECTION0006000000000000000> Installing ALSCRIPT</A>
+<LI> <A NAME=tex2html10 HREF=section3_7.html#SECTION0007000000000000000> Brief Description of ALSCRIPT</A>
+<LI> <A NAME=tex2html11 HREF=section3_8.html#SECTION0008000000000000000> New Features in Version 1.4.4</A>
+<LI> <A NAME=tex2html12 HREF=section3_9.html#SECTION0009000000000000000> New Features in Version 1.4.5 - Program alsnum</A>
+<LI> <A NAME=tex2html13 HREF=section3_10.html#SECTION00010000000000000000> New Features in Version 2.0</A>
+<UL> 
+<LI> <A NAME=tex2html14 HREF=subsection3_10_1.html#SECTION00010100000000000000> New Step 1 Commands</A>
+<LI> <A NAME=tex2html15 HREF=subsection3_10_2.html#SECTION00010200000000000000> New Step 2 Commands</A>
+<LI> <A NAME=tex2html16 HREF=subsection3_10_3.html#SECTION00010300000000000000> New special TEXT commands</A>
+</UL> 
+<LI> <A NAME=tex2html17 HREF=section3_11.html#SECTION00011000000000000000> Running ALSCRIPT</A>
+<UL> 
+<LI> <A NAME=tex2html18 HREF=subsection3_11_1.html#SECTION00011100000000000000> Basic Use</A>
+<LI> <A NAME=tex2html19 HREF=subsection3_11_2.html#SECTION00011200000000000000> More complex effects - Text Lines, and Masks</A>
+</UL> 
+<LI> <A NAME=tex2html20 HREF=section3_12.html#SECTION00012000000000000000> Using Colour</A>
+<LI> <A NAME=tex2html21 HREF=section3_13.html#SECTION00013000000000000000> The MASK command family</A>
+<UL> 
+<LI> <A NAME=tex2html22 HREF=subsection3_13_1.html#SECTION00013100000000000000> Summary of mask commands</A>
+</UL> 
+<LI> <A NAME=tex2html23 HREF=section3_14.html#SECTION00014000000000000000> Printing ALSCRIPT Files</A>
+<LI> <A NAME=tex2html24 HREF=section3_15.html#SECTION00015000000000000000> Conclusion</A>
+<LI> <A NAME=tex2html25 HREF=section3_16.html#SECTION00016000000000000000> Appendices</A>
+<UL> 
+<LI> <A NAME=tex2html26 HREF=subsection3_16_1.html#SECTION00016100000000000000> ALSCRIPT Command Summary</A>
+<UL> 
+<LI> <A NAME=tex2html27 HREF=subsubsection3_16_1_1.html#SECTION00016110000000000000> STEP 1 COMMANDS</A>
+<LI> <A NAME=tex2html28 HREF=subsubsection3_16_1_2.html#SECTION00016120000000000000> REQUIRED STEP 1 COMMANDS</A>
+<LI> <A NAME=tex2html29 HREF=subsubsection3_16_1_3.html#SECTION00016130000000000000> OPTIONAL STEP 1 COMMANDS</A>
+<LI> <A NAME=tex2html30 HREF=subsubsection3_16_1_4.html#SECTION00016140000000000000> STEP 2 COMMANDS</A>
+</UL> 
+<LI> <A NAME=tex2html31 HREF=subsection3_16_2.html#SECTION00016200000000000000> AMPS Block file format</A>
+<LI> <A NAME=tex2html32 HREF=subsection3_16_3.html#SECTION00016300000000000000> PostScript Fonts</A>
+<LI> <A NAME=tex2html33 HREF=subsection3_16_4.html#SECTION00016400000000000000> 386 DOS installation</A>
+<LI> <A NAME=tex2html34 HREF=subsection3_16_5.html#SECTION00016500000000000000> TECHNICAL NOTES</A>
+<LI> <A NAME=tex2html35 HREF=subsection3_16_6.html#SECTION00016600000000000000> Unix Installation</A>
+<LI> <A NAME=tex2html36 HREF=subsection3_16_7.html#SECTION00016700000000000000> VAX/VMS Installation</A>
+<LI> <A NAME=tex2html37 HREF=subsection3_16_8.html#SECTION00016800000000000000> Alternative ways of invoking ALSCRIPT</A>
+<LI> <A NAME=tex2html38 HREF=subsection3_16_9.html#SECTION00016900000000000000> Program Crashes and Known Bugs</A>
+<LI> <A NAME=tex2html39 HREF=subsection3_16_10.html#SECTION000161000000000000000> Wish List for next version!!</A>
+<LI> <A NAME=tex2html40 HREF=subsection3_16_11.html#SECTION000161100000000000000> Acknowledgements</A>
+<LI> <A NAME=tex2html41 HREF=subsection3_16_12.html#SECTION000161200000000000000> References</A>
+</UL> 
+<LI> <A NAME=tex2html42 HREF=section3_17.html#SECTION00017000000000000000>  <em>About this document ...</em> </A>
+</UL>
+<HR>
+
+</BODY>
+<P><ADDRESS>
+gjb@bioch.ox.ac.uk
+</ADDRESS>
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