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+<HEAD>
+<TITLE> Basic Use</TITLE>
+</HEAD>
+<BODY><P>
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+<B> Next:</B> <A NAME=tex2html247 HREF=subsection3_11_2.html> More complex effects </A>
+<B>Up:</B> <A NAME=tex2html245 HREF=section3_11.html> Running ALSCRIPT</A>
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+<HR> <P>
+<H2><A NAME=SECTION00011100000000000000> Basic Use</A></H2>
+<P>
+I recommend you read through this section, then scan the commands in
+<A HREF=subsection3_16_1.html#app1>ALSCRIPT Command Summary</A> to get a feel for what ALSCRIPT can do.
+<P>
+See <A HREF=subsection3_16_8.html#app7>Alternative ways of invoking ALSCRIPT</A>. In this section, the
+interactive method is described. The QUICK START method shown in
+<A HREF=subsection3_16_8.html#app7>Alternative ways of invoking ALSCRIPT</A>
+is useful to format a sequence alignment quickly
+using standard pointsize and shading.
+<P>
+ALSCRIPT is designed to work with AMPS block file format multiple
+alignments. If you have a multiple alignment generated by CLUSTAL V
+or the GCG package, then it must be translated to AMPS block file
+format.
+<P>
+To translate a GCG .MSF file: Type: msf2blc.
+To translate a CLUSTAL PIR format file, or any PIR format file: clus2blc.
+<P>
+Both programs prompt for the name of an input file, and an output
+block file name. A good convention to follow is to name all blockfiles
+with the extension ".blc".
+<P>
+To run ALSCRIPT simply type:
+<P>
+alscript
+<P>
+you will then be prompted for the name of the ALSCRIPT command file.
+Having typed the filename, the commands will be executed as you have
+specified.
+<P>
+A Simple Command File (example.als)
+<P>
+The file example.blc contains a small multiple sequence alignment.
+The following ALSCRIPT command file will convert this into a
+PostScript alignment file in 12 point Helvetica.
+<P>
+<PRE><TT>
+#Comments in ALSCRIPT command files start with a #
+#
+#Commands are free format - separated by blank, tab or comma characters
+#
+BLOCK_FILE example.blc #define the block file to format
+OUTPUT_FILE example.ps #where to put the result
+LANDSCAPE #landscape paper orientation
+POINTSIZE 12 #12 point default pointsize
+DEFINE_FONT 0 Helvetica DEFAULT #set font 0 to be Helvetica
+SETUP #Tell the program to get on with it.</TT></PRE>
+<P>
+Now try changing the POINTSIZE value to 5 ALSCRIPT will re-format the
+alignment to make best use of the available paper.
+<P>
+These are all STEP 1 commands - they refer to overall layout, and system
+settings - for example, the paper size or maximum sequence length.
+Other commonly used STEP 1 commands are IDENT_WIDTH which reserves more
+or less width for the sequence identifier codes, NUMBER_SEQS which adds
+a number to each sequence and LINE_WIDTH_FACTOR which allows the
+thickness of all boxing lines to be adjusted. See
+<A HREF=subsection3_16_1.html#app1>ALSCRIPT Command Summary</A>
+for details of these and all other STEP 1 commands.
+<P>
+The simple example outlined above can be modified with a variety of
+STEP 2 commands.
+<P>
+for example file example2.als:
+<P>
+<PRE><TT>
+# FILE example2.als
+#
+#Commands are free format - separated by blank, tab or comma characters
+#
+BLOCK_FILE example.blc #define the block file to format
+OUTPUT_FILE example2.ps #where to put the result
+LANDSCAPE #landscape paper orientation
+POINTSIZE 12 #12 point default pointsize
+DEFINE_FONT 0 Helvetica DEFAULT #set font 0 to be Helvetica
+DEFINE_FONT 1 Helvetica REL 0.5 #set font 1 to be half sized Helvetica
+DEFINE_FONT 3 Helvetica-Bold DEFAULT #set font 3 to be Bold Helvetica
+DEFINE_FONT 4 Times-BoldItalic DEFAULT #font 4 is Times-BoldItalic
+NUMBER_SEQS #Number the sequences at left hand side
+SETUP #Tell the program to get on with it.
+#
+#step 2 commands come after the SETUP command
+#
+#Here are some examples...
+#
+SURROUND_CHARS GP ALL #draw lines around all G and P
+SHADE_CHARS ILVW ALL 0.6 #shade all I L V and W with value 0.6
+BOX_REGION 1 1 2 20 0.8 #rectangular box from positions 1 to 2 of sequences 1 to 20
+FONT_CHARS C ALL 3 #Use font 3 (BOLD Helvetica) for C characters
+ID_FONT ALL 1 #set identifiers in font 1</TT></PRE>
+<P>
+There are many possible ways of combining these commands and the
+others shown in
+<A HREF=subsection3_16_1.html#app1>ALSCRIPT Command Summary</A>.
+In general, if you apply multiple
+commands to the same residue, the effect of the last applied command
+persists where there would otherwise be a conflict. Thus the
+intersection of two overlapping SHADed regions would be shaded
+according to the second SHADE command, not some mixture of the two.
+Similarly for FONT commands. BOX and SURROUND commands behave in the
+opposite sense, all BOXing and SURROUNDing persists regardless of how
+many commands you issue. This makes it possible for example, to
+SURROUND two different sets of residues as follows:
+<P>
+<PRE><TT>
+
+SURROUND_CHARS DE ALL
+SURROUND_CHARS DEHKR ALL</TT></PRE>
+<P>
+This would result in D and E characters being partitioned from the rest as well
+as D E H K R characters (see Example output).
+<P>
+<HR> <A NAME=tex2html246 HREF=subsection3_11_2.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/next_motif.gif"></A> <A NAME=tex2html244 HREF=section3_11.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/up_motif.gif"></A> <A NAME=tex2html238 HREF=section3_11.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/previous_motif.gif"></A> <A NAME=tex2html248 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=tex2html247 HREF=subsection3_11_2.html> More complex effects </A>
+<B>Up:</B> <A NAME=tex2html245 HREF=section3_11.html> Running ALSCRIPT</A>
+<B> Previous:</B> <A NAME=tex2html239 HREF=section3_11.html> Running ALSCRIPT</A>
+<HR> <P>
+<HR>
+
+</BODY>
+<P><ADDRESS>
+gjb@bioch.ox.ac.uk
+</ADDRESS>
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