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+<HEAD>
+<TITLE> Alternative ways of invoking ALSCRIPT</TITLE>
+</HEAD>
+<BODY><P>
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+<H2><A NAME=SECTION00016800000000000000> Alternative ways of invoking ALSCRIPT</A></H2>
+<P>
+<A NAME=app7><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/invis_anchor.xbm"></A>
+<P>
+The documentation above describes the interactive mode of running ALSCRIPT.
+However, it may be more convenient to run the program as a pipe under
+Unix or MS-DOS. Examples are shown here.
+<P>
+ALSCRIPT is a program for producing pretty versions of multiple
+sequence aligments. ALSCRIPT will also format single sequences. A
+full description of the program is given in the file "alscript.doc".
+<P>
+Ways of running alscript:
+<P>
+<OL><LI>
+ Interactive mode: just type alscript.
+ You will be prompted for a command file name. The command file will
+ define the AMPS blocfile, and name of the file to store the PostScript
+ output - see alscript.doc for details.
+<P>
+<LI>
+ alscript <command_file> has same effect as 1, But does not prompt for
+ the command file
+ e.g. alscript example1.als
+<P>
+<LI>
+ alscript -q < <blocfile> > <PostScript>
+ Quick mode - uses default commands, reads alignment from stdin,
+ writes PostScript to stdout. This mode creates a command file
+ called ALPSQ.COM.
+<P>
+ e.g. alscript -q < example1.blc > example1.ps
+<P>
+<LI>
+ alscript -f <command_file>
+ Similar effect to 2.
+<P>
+<LI>
+ alscript -f <command_file> -s
+ Silent operation: No messages are written to stderr, unless fatal.
+ Silent operation may be toggled by the silent_mode command
+ in the command file.
+<P>
+<LI>
+ alscript -f <command_file> -p < <blocfile> > <PostScript>
+ Make alscript work like a pipe - blocfile is read from stdin,
+ postscript is written
+ to stdout. Messages are written to stderr. To supress messages include
+ the -s flag too
+<P>
+ e.g. alscript -f example1.als -p -s < example1.blc > example1.ps
+<P>
+</OL>
+<P>
+Using alscript as a pipe has the advantage of allowing the blocfile to
+be created on the fly by the programs msf2blc or clus2blc. For example
+if we have a GCG .msf file called "pileup.msf" we can run alscript with
+default shading/fonts and send the results straight to the PostScript
+printer "lpr" as follows:
+<P>
+msf2blc -q <pileup.msf | alscript -q -s | lpr
+<P>
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+<B> Next:</B> <A NAME=tex2html471 HREF=subsection3_16_9.html> Program Crashes and </A>
+<B>Up:</B> <A NAME=tex2html469 HREF=section3_16.html> Appendices</A>
+<B> Previous:</B> <A NAME=tex2html463 HREF=subsection3_16_7.html> VAX/VMS Installation</A>
+<HR> <P>
+<HR>
+
+</BODY>
+<P><ADDRESS>
+gjb@bioch.ox.ac.uk
+</ADDRESS>
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