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+\documentstyle[12pt,times,html]{article}
+\begin{document}
+\parindent 0in
+%\raggedright
+\bibliographystyle{jmb}
+\nocite{TitlesOn}
+\begin{titlepage}
+%\begin{singlespace}
+\begin{center}
+\begin{Huge}
+\begin{bf}
+\vskip 0.5in
+
+User Guide to
+
+ALSCRIPT - Sequence alignment to PostScript\\
+
+Version 2.03\\
+
+\end{bf}
+\end{Huge}
+
+\vskip 0.5in
+
+\begin{large}
+{\em Geoffrey J. Barton}
+\vskip 0.5in
+
+
+Laboratory of Molecular Biophysics\\
+University of Oxford\\
+Rex Richards Building\\
+South Parks Road\\
+Oxford OX1 3QU\\
+U.K.\\
+
+\vskip 0.25in
+
+\end{large}
+\vskip 0.25in
+Tel: (44) 1865-275368\\
+Fax: (44) 1865-510454\\
+e-mail: gjb@bioch.ox.ac.uk
+
+\vskip 0.25in
+
+REFERENCE:\\
+ Barton, G. J. (1993),\\
+ ALSCRIPT a tool to format multiple sequence alignments\\
+ Protein Engineering, Volume 6, No. 1, pp.37-40.\\
+\vskip 0.25in
+
+\end{center}
+\end{titlepage}
+\tableofcontents
+
+\section{Update History}
+\begin{verbatim}
+
+VERSION 1.0 19 June 1992
+Version 1.1 26 June 1992
+Version 1.2 21 October 1992: Add multiple blocks per page option.
+Version 1.3 15 November 1992: First Distribution.
+Version 1.4 6 December 1992: Add Colour commands.
+Version 1.4.1 1 February 1993: Small bug fixes - FULL RELEASE VERSION.
+Version 1.4.2 15 February 1993: Make silent_mode toggle.
+Version 1.4.3 1 March 1993: Fix bug in colour option.
+Version 1.4.4 24 March 1993: Add mask features (should be version 1.5).
+Version 1.4.5 25 May 1993: Include alsnum program in distribution.
+ 7 June 1993: Fix NO_NUMBERS bug in documentation
+ Change defaults for -q option to use MASK.
+
+Version 2.0 23 May 1995: Numerous changes and additions including the
+ option to colour backgrounds
+ differently, ommission of idents on
+ second and subsequent lines, helix,
+ strand and other special characters,
+ relative numbering, error checking of
+ ranges on input, bounding box,
+ screening, conservation colouring...
+Version 2.03 5 June 1996: Small bug fixes - patches incorporated.
+ BACKGROUND_REGION and BOUNDING_BOX commands moved to
+ step 1 section.
+
+\end{verbatim}
+
+\section{Read This First - VERSION 2.0}
+
+This manual describes an interim release of ALSCRIPT that includes
+many additional features over the previously distributed Version
+1.4.5. I had hoped to make a lot more changes and improvements before
+distributing the new version, however I have not had the time to do
+this. I am distributing Version 2.0 since the new features have been
+used in a number of published alignment figures. Please see
+\hyperref{New Features in Version 2.0}{see the Section }{ }{new2} for details
+of the new features.
+
+\section{Related Programs}
+
+The AMPS package (Barton, 1990). This performs multiple sequence
+alignments and databank scanning.
+
+AMAS (Livingstone and Barton, 1993, CABIOS, 9, 745-756). Analysis of
+Multiply Aligned Sequences. This package uses a sophisticated
+set-based method to identify patterns of residue conservation in
+multiple sequence alignments.
+
+All programs are available by anonymous ftp from geoff.biop.ox.ac.uk.
+Please see the README file for details licencing and registration.
+You can read manuals for the programs and some related papers at
+http://geoff.biop.ox.ac.uk/.
+
+\section{Availability}
+
+ALSCRIPT is available free of charge for academic and non-commercial
+purposes. Distribution is by anonymous ftp from geoff.biop.ox.ac.uk.
+See the README file on the ftp server for details. You need to
+register with G. J. Barton before downloading the software.
+
+\section{Installing ALSCRIPT}
+
+See the appropriate section for the computer type you are using:
+
+For PCs see \hyperref{386 MS-DOS installation}{see Section }{}{app4}.
+For Unix see \hyperref{Unix installation}{see Section }{ }{app5}.
+For VMS see \hyperref{VMS installation}{see Section }{ }{app6}.
+
+\section{Brief Description of ALSCRIPT}
+
+ALSCRIPT takes a multiple sequence alignment in AMPS (Barton \&
+Sternberg, 1987, Barton, 1990) block-file format and a set of
+formatting commands and produces a PostScript file that may be printed
+on a PostScript laser printer, or viewed using a PostScript previewer
+(e.g. Sun Microsystem's PageView program). CLUSTAL and GCG format
+multiple alignment files may also be used (see below). ALSCRIPT is NOT a
+multiple sequence alignment program, nor is it an alignment editor.
+
+Given a block-file and pointsize (character width/height), ALSCRIPT
+calculates how many residues can be fitted across the page, and how
+many sequences will fit down the page, it then prints the alignment at
+the chosen pointsize on as many pages as are needed. Running ALSCRIPT with
+a smaller or larger pointsize will automatically re-scale the alignment
+to fit on fewer or more pages as appropriate. The actual page
+dimensions may be re-set to any value, so if you have access to an A3
+PostScript printer, or typesetting machine, alignments can readily be
+scaled to maximise the available space.
+
+Each output page has three basic regions. The left hand edge contains
+identifier codes for each sequence. The main part of the page holds the
+alignment, and the top part, the position numbers and tick marks. ALSCRIPT
+commands make use of a character coordinate system for font changes,
+and other formatting commands. Thus, any residue in the alignment may
+be referred to by its sequence position number (x-axis) and sequence
+number (y-axis), similarly, ranges of residue positions, or sequences
+may also be defined in the character coordinate system.
+
+The basic ALSCRIPT commands allow the following functionality:
+
+Fonts: Any PostScript font at any size may be defined and used on
+individual residues, regions or identifier codes.
+
+Boxing: Simple rectangular boxes may be drawn around any part of the
+alignment. Particular residue types may be selected and automatically
+"surrounded" by lines. For example, if the characters 'G' and 'P' are
+selected, then lines will not be drawn between G and P characters, but
+only where G and P border with other characters.
+
+Shading: Grey shading of any level from black to white may be applied
+to any region of the alignment, either as a rectangular region, or as
+residue specific shading. e.g. "shade all Cys residues between
+positions 6 and 30"
+
+Text: Specific text strings may be added to the alignment at any
+position and in any font or font size.
+
+Lines: Horizontal or vertical lines may be drawn to the left, right, top
+or bottom of any residue position or group of positions.
+
+Colour: Characters or character backgrounds may be independently
+coloured.
+
+The example block file "example1.blc" and command file "example1.als"
+illustrate most of these commands in action.
+
+Although written with the aim of producing figures for journal
+submission, ALSCRIPT may be used as a tool for interpreting multiple
+sequence alignments. For example, the boxing, shading and font changing
+facilities can be applied to highlight amino acids of a particular type
+and thus draw attention to clusters of positive or negative charge,
+hydrophobics, etc.
+
+
+\section{New Features in Version 1.4.4}
+
+This version introduces the MASK family of commands which allows
+boxing, shading etc to be applied according to the frequency of
+occurence of the character types at each position in the alignment.
+For example, it is possible to box positions where one character is
+seen in more than N of the sequences. It is also possible to
+box/shade etc the most frequently occurring character at each
+position. Commands exist to select which characters will be used in
+the calculation of frequencies and which will be excluded, thus boxing
+can be based upon two or more character types at a position. MASK
+commands also exist to show residues identical to one sequence in the
+set. See the section on MASK below for details.
+
+NOTE: Although boxing according to the frequency of amino acids seen
+at a position is a popular method of representation it is not usually
+the most informative. An analysis that takes into account the
+physico-chemical properties of the amino acids and also relates the
+amino acid similarities to the overall similarity between the
+sequences is more helpful in identifying functionally important
+residues. The AMAS program (Livingstone and Barton, 1993) applies a
+flexible hierarchical set-based approach to this problem.
+
+\section{New Features in Version 1.4.5 - Program alsnum}
+
+Version 1.4.5 includes the program "alsnum". This is a temporary solution to
+the residue numbering problem. Ultimately, these functions will be included
+as alscript commands.
+
+alsnum creates a set of TEXT commands that can be incorporated into an
+alscript command file to place sequential numbers at any position in the
+alignment. The numbers ignore gaps, so the numbering will correspond to
+the specific sequence position rather than the alignment.
+
+To use the program:
+
+1. Decide where you want the numbers to be placed. For example, you might
+want the numbers above the third sequence in the alignment. If so, make
+an extra sequence space above the third sequence using the ADD\_SEQ\ command.
+
+2. Decide what is the number of the first residue of the sequence to be
+numbered. This will not always be 1 since you may be aligning fragments
+or domains.
+
+3. Decide the numbering interval (e.g. every 10th amino acid).
+
+4. Run the program.
+
+For example, if you want to add numbers according to sequence 37 of a
+block file (junk.blc), calling the first residue of the sequence 12,
+and with an interval of 5, and the numbers are to be placed at the
+location of sequence 3 in the alignment. Type:
+
+alsnum 37 12 5 3 $<$ junk.blc $>$ junk.text
+
+5. Add the resulting TEXT commands from junk.text to your alscript
+command file.
+
+\section{New Features in Version 2.0}
+\label{new2}
+
+Error checking is now done on all ranges input. If you run ALSCRIPT
+2.0 on a file that worked with ALSCRIPT 1.4.5, and it complains about
+out of range numbers, then check your ranges carefully. If you think
+you are right, then send me a minimal example of the problem and I
+will investigate. Versions of ALSCRIPT before 2.0 would often work
+happily with out of range numbers and produce perfectly OK output.
+
+The files {\bf ipns.als} and {\bf ipns.blc} show example command and
+block file that use most of these new commands. See the {\em
+examples} directory.
+
+\subsection{New Step 1 Commands}
+
+SCREENSIZE 120
+
+Usually you should not need to change this value, it alters the
+screening used by the printer. A value of 120 is used by default. On
+most 300dpi black and white printers this gives much smoother greys
+than the default used in earlier versions of ALSCRIPT.
+
+PIR\_SAVE\ filename
+
+Will cause the block file to be saved into the file ``filename'' in
+PIR format. This can be useful for moving block file alignments to other
+programs.
+
+MSF\_SAVE\ filename
+
+Will cause the block file to be saved into the file ``filename'' in
+something that approximates GCG .msf format. {\em Warning! This has not
+been fully tested.}
+
+NUMBER\_COLOUR\ 4
+
+Sets the colour used for numbering at the top of the alignment (no
+American spelling at the moment). In this example, colour number 4 has been
+defined (See the DEFINE\_COLOUR command if you are not sure what this means).
+
+SINGLE\_PAGE
+
+If this is set, ALSCRIPT assumes everything will be plotted on one
+page. At the moment, all this does is write the bounding box for the
+figure, so encapsulating the PostScript. This {\em may} allow the
+output of alscript to be imported into word processors etc, but
+probably not all.
+
+ID\_ONLY\_ON\_FIRST\_LINE
+
+If this is present, then sequence identifiers will only be printed on
+the first line of the alignment. Often this looks better for small
+alignments than the default.
+
+BACKGROUND\_COLOUR\ 7
+
+Sets the colour used for the background to the alignment. This can be
+useful for preparing figures for projection. At the moment this only
+works reliably when the SINGLE\_PAGE is also set.
+
+
+BOUNDING\_BOX\ x\ y\ x1\ y1
+
+Defines the bounding box for the figure. This is set in points (1/72 inch).
+NOTE: In version 2.0 this was a STEP 2 Command.
+
+BACKGROUND\_REGION\ x\ y\ x1\ y1
+
+Defines the region to colour as background - the default is set up for A4 paper
+so US users may have to fiddle with this. Values are points (1/72 inch).
+NOTE: In version 2.0 this was a STEP 2 Command.
+
+\subsection{New Step 2 Commands}
+
+
+COLOUR\_TEXT\_REGION\ x\ y\ x1\ y1 colour
+
+Sets the colour for TEXT command output. Similar syntax to COLOUR\_REGION, FONT\_REGION etc.
+
+COLOUR\_LINE\_REGION\ x\ y\ x1\ y1 colour
+
+Set the colour for LINEs in a region.
+
+CALCONS\ x\ y\ x1\ y1
+
+Calculate conservation values according to Zvelebil {\em et al.} for the designated
+region. (See Livingstone \& Barton 1993 for details and further refs)
+
+MASK\ CONSERVATION\ cutoff
+
+If CONSCAL has been used, then mask residues according to the conservation cutoff.
+
+e.g. MASK CONSERVATION 10 would mask all identities, MASK CONSERVATION 6 would
+mask reasonably conserved positions. See examples for more on this command.
+
+HELIX\ x1\ y\ x2
+
+Draw a helix from x1 to x2 of sequence y.
+
+STRAND\ x1\ y\ x2
+
+Draw a strand from x1 to x2 of sequence y.
+
+COIL\ x1\ y\ x2
+
+Draw a coil (horizontal line) from x1 to x2 of sequence y.
+
+RELATIVE\_TO <seqnum> <startnum>
+
+Set reference numbers to work relative to sequence number <seqnum>. This
+means that in all subsequent commands, ALSCRIPT will translate your x
+values into absolute position values in the alignment. This is {\em
+extremely} useful since you can annotate your alignment using your
+favourite sequences as a reference point. You no longer have to
+translate every x position into the alignment position.
+
+<startnum> is optional. If present, it specifies what the first
+residue in the displayed sequence is. For example, you may be showing
+residues 200-500 of a sequence, so <startnum> would be 200 rather than
+the default of 1. {\em Warning - this is a very new feature and
+bounds checking is not fully enabled for it}.
+
+You can use RELATIVE\_TO several times in the command file to annotate
+different sequences. RELATIVE\_TO 0 resets to the ``normal''
+alignment numbering.
+
+\subsection{New special TEXT commands}
+
+Some special TEXT commands have been added to allow drawing of alternative
+shapes etc. In fact this is how the HELIX, STRAND and COIL commands are implemented. The text commands are all prefixed by an @ symbol.
+
+e.g. TEXT 3 6 ``@fuparrow''
+
+will draw a filled up arrow at position 3,6.
+
+The alternative text commands are:
+
+@leftarrow - an open left pointing arrow.
+
+@fleftarrow - a filled left pointing arrow.
+
+@uparrow - an open up pointing arrow.
+
+@fuparrow - a filled up pointing arrow.
+
+@downarrow - an open down pointing arrow.
+
+@fdownarrow - a filled down pointing arrow.
+
+@circle - an open circle.
+
+@fcircle - a filled circle.
+
+I plan to make this option more flexible in the near future.
+
+\section{Running ALSCRIPT}
+\subsection{Basic Use}
+
+I recommend you read through this section, then scan the commands in
+\hyperref{ALSCRIPT Command Summary}{Section }{ }{app1} to get a feel for what ALSCRIPT can do.
+
+See \hyperref{Alternative ways of invoking ALSCRIPT}{Section }{for
+alternative methods of invoking ALSCRIPT}{app7}. In this section, the
+interactive method is described. The QUICK START method shown in
+\hyperref{alternative ways of invoking ALSCRIPT}{Section }{ }{app7}
+is useful to format a sequence alignment quickly
+using standard pointsize and shading.
+
+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.
+
+To translate a GCG .MSF file: Type: msf2blc.
+To translate a CLUSTAL PIR format file, or any PIR format file: clus2blc.
+
+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".
+
+To run ALSCRIPT simply type:
+
+alscript
+
+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.
+
+A Simple Command File (example.als)
+
+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.
+
+\begin{verbatim}
+#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.
+\end{verbatim}
+
+Now try changing the POINTSIZE value to 5 ALSCRIPT will re-format the
+alignment to make best use of the available paper.
+
+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
+\hyperref{ALSCRIPT Command Summary}{Section }{ }{app1}
+for details of these and all other STEP 1 commands.
+
+The simple example outlined above can be modified with a variety of
+STEP 2 commands.
+
+for example file example2.als:
+
+\begin{verbatim}
+# 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
+
+\end{verbatim}
+
+There are many possible ways of combining these commands and the
+others shown in
+\hyperref{ALSCRIPT Command Summary}{Section }{ }{app1}.
+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:
+
+\begin{verbatim}
+
+SURROUND_CHARS DE ALL
+SURROUND_CHARS DEHKR ALL
+
+\end{verbatim}
+
+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).
+
+\subsection{More complex effects - Text Lines, and Masks}
+
+Text, lines and masking are meant to be used to annotate the multiple
+alignment. The TEXT command allows any piece of text to be located
+anywhere on the alignment. Clearly, however it makes little sense to
+superimpose the text over the alignment though this can be done! Accordingly,
+you must first make a space to put the text in. Usually, this will be a
+few lines below the multiple sequence alignment, but you may want to
+add text at the top, or somewhere in between two sequences. You can make
+space in two ways. Either by editing the block-file to introduce "dummy"
+sequences at the locations you want, or by making use of the ADD\_SEQ\
+command.
+
+The ADD\_SEQ\ command has two arguments, the sequence after which you want
+further sequences to be added, and how many blank sequences you need.
+Thus, we can reserve space for 5 lines of text underneath a 10 sequence
+multiple alignment with the following command.
+
+ADD\_SEQ\ 10 5
+
+we can then put text below the alignment at the 20th residue.
+
+TEXT 20 13 "Active Site His"
+
+or any other position.
+
+Similarly, we could draw a vertical line to point out which residue we mean
+
+LINE LEFT 20 13 11
+
+And change the font of the text to number 7 (whatever that has been set to):
+
+FONT\_RESIDUE\ 20 13 7
+
+You can have multiple ADD\_SEQ\ commands, but they must occur in sequence order.
+Thus:
+
+\begin{verbatim}
+ADD_SEQ 0 5
+ADD_SEQ 5 12
+\end{verbatim}
+is legal.
+But
+\begin{verbatim}
+ADD_SEQ 5 12
+ADD_SEQ 0 5
+\end{verbatim}
+
+Is NOT!! NO CHECKING IS performed by the program for this error - so beware!
+
+Note that add\_seq\ commands refer to the actual sequence number as
+implied by the block file, not the number after applying the add\_seq\
+command. Thus, for a four sequence block file, if you want to add
+space for three sequences before sequence 1 and two sequences after
+sequence 3, the commands would be:
+
+\begin{verbatim}
+ADD_SEQ 0 3
+ADD_SEQ 3 2
+\end{verbatim}
+
+Text added with the TEXT command will not be split across page breaks,
+so you may in some circumstances need to fiddle a little with the
+location/pointsize for the text to get the desired result.
+
+Masking is a technique for drawing irregular shaped outlines, or
+shaded regions - this should not be confused with the MASK family of commands
+described below. For example a histogram can be added to the bottom of
+an alignment by first defining some dummy sequences in the block-file
+that have letters building up the shape of the histogram, then using
+the SURROUND\_CHARS\ or SHADE\_CHARS\ commands together with the SUB\_CHARS\
+command to produce the desired effect. An example of this operation
+being used to show frequencies of secondary structure predictions is
+shown in example1.als and in the Protein Engineering paper.
+
+\section{Using Colour}
+
+Version 1.4 includes commands to allow the independent colouring of
+characters, or their backgrounds. Colours are defined in a similar
+manner to fonts using the DEFINE\_COLOUR\ command (American spelling also
+allowed). For example:
+
+DEFINE\_COLOUR\ 7 1 0 0
+
+defines colour number 7 to be red - see
+\hyperref{ALSCRIPT Command Summary}{Section }{ }{app1}
+for full details of
+this command. Colours 99 and 100 are pre-defined to white and black.
+ALSCRIPT assumes the paper colour is white.
+
+The command to colour the text of a character or text string is:
+
+CCOL\_CHARS\
+
+the command to colour the background of a character is
+
+SCOL\_CHARS\
+
+both have similar syntax to the FONT\_CHARS command.
+
+COLOUR\_REGION\ and COLOUR\_RES\ have similar syntax to SHADE\_REGION\ and
+SHADE\_RES.
+
+An example command file that uses colour is shown in example3.als.
+
+\section{The MASK command family}
+
+The idea behind the MASK command is to build up a set of character
+positions that will subsequently be boxed, shaded, set in a particular
+font, etc. For example, lets say we want to box the most frequently
+occuring character at each position in an alignment.
+
+The command
+
+mask SETUP
+
+tells ALSCRIPT to prepare a mask.
+
+mask FRE ALL
+
+specifies that the most frequently occuring character at each position
+in the alignment will be masked. This command can be restricted to a
+region of the alignment using: mask FRE sx sy ex ey, where sx etc
+define the region in the same way as for font\_region\ and other commands.
+
+mask BOX ALL
+
+Tells ALSCRIPT to create the boxing lines that will separate the masked
+characters from non-masked characters - this command may also be
+restricted to a region of the alignment.
+
+The mask can be reset for re-use using the command:
+
+mask RESET
+
+Two further commands define which characters can be used when
+calculating the mask. This allows gap-characters, or other amino acids
+to be excluded from the calculation to avoid unwanted boxing.
+
+mask LEGAL "AVLI"
+
+defines the AVL and I as the only characters that will be used when
+calculating the mask.
+
+mask ILLEGAL ".-\_"
+
+defines .- and \_\ as characters that will not be used when calculating
+the mask. NOTE: the blank character " " cannot be defined in this way.
+To avoid boxing " " characters substitute blanks for something else
+(using SUB\_CHARS),\ calculate the mask, then substitute back.
+
+\subsection{Summary of mask commands}
+
+mask SETUP
+\# Prepares for masking
+
+mask LEGAL $<$qstring$>$
+\# defines characters to include in ID or FRE calcs - optional.
+
+mask ILLEGAL $<$qstring$>$
+\# defines characters to exclude in ID or FRE calcs - optional.
+
+mask ID ALL N
+\# Calculates a mask that flags the character that occurs at least N
+times at a position. The word ALL can be substituted by four numbers
+that define a region of the alignment.
+
+mask FRE ALL
+\# calculates a mask that flags the most frequently occuring amino acid
+at each position. ALL may be replaced by four numbers defining a region
+of the alignment.
+
+Multiple mask FRE or mask ID commands may be applied, using different
+LEGAL and ILLEGAL character definitions. In this way more complex
+effects can be built up.
+
+The mask command also allows characters that are identical to one
+sequence to be masked.
+
+mask AGREE ALL N
+
+will mask all positions that are identical to the Nth sequence. Thus,
+for sequences that are very similar to a newly sequenced sequence, all
+characters identical to the new sequence can be boxed or shaded, or set
+in a different font or colour etc...
+
+mask NOT ALL
+
+allows the mask to be inverted. Thus, all positions that are NOT in the
+mask now form the mask. So, having done a mask AGREE, a mask NOT will
+allow the positions that are not identical to the selected sequence to
+be highlighted or substituted.
+
+mask SUB ALL $<$char$>$
+
+substitutes all characters in the mask with the character $<$char$>$.
+
+mask REGION ALL
+applies a mask to all residues in the defined region.
+
+The following effects can now be applied to the masked characters:
+
+mask BOX ALL
+\# boxes the masked residues - ie surrounds them by lines.
+
+mask SHADE ALL $<$grey$>$
+\# shades the masked residues by grey value.
+
+mask FONT ALL $<$fontnum$>$
+\# Uses font fontnum to output the masked residues.
+
+mask INVERSE ALL
+\# Inverts the masked characters - ie outputs them in white.
+
+mask CCOL ALL $<$colnum$>$
+\# outputs the masked characters in the defined colour.
+
+mask SCOL ALL $<$colnum$>$
+\# outputs the backgrounds of the masked characters in the defined
+colour.
+
+In all commands, the word ALL can be replaced by four numbers defining
+the region to which the command is applied.
+
+mask RESET
+\# resets the entire mask for re-use
+
+
+\section{Printing ALSCRIPT Files}
+
+ALSCRIPT produces files in PostScript which may be printed on a PostScript
+printer (e.g. an Apple LaserWriter). If you don't have a PostScript printer,
+then you may still be able to use ALSCRIPT if you get hold of the
+GhostScript software. This is a free package that interprets PostScript
+commands and can produce output on a large number of different types of
+printer. GhostScript runs on most hardware types (including PCs) and can also
+display output to the screen. The package can be obtained from many different
+sites on the Internet (In the UK try src.doc.ic.ac.uk).
+
+The actual command you need to type to send a PostScript file to the printer
+will depend on your system. Consult your system manager for help.
+
+Be warned, ALSCRIPT can create extremely large PostScript files if
+lots of boxing and shading is done on big alignments. On older
+printers such output may take a long time to process.
+
+\section{Conclusion}
+
+ALSCRIPT provides a powerful set of formatting and editing commands
+specifically tailored for multiple sequence alignments. It is best
+used in conjunction with a PostScript previewer such as Sun's
+PageView or GhostView since this allows the effect of changing a command to be
+seen quickly. In the absence of such a tool, simpler effects can be
+tested out without destroying too many trees in the Laser Printer!
+
+Like most programs, ALSCRIPT is evolving as I find new problems to display, so
+if you have any suggestions - I shall endeavour to include them in a later
+version.
+
+\section{Appendices}
+
+\subsection{ALSCRIPT Command Summary}
+\label{app1}
+
+WARNING: Very little error checking is performed on command input. If
+you give the wrong number of arguments to a command, then unexpected
+things may happen, or the program will crash very inelegantly. I hope
+to fix this in the next version of the program, in the meantime, make sure
+you give the correct number of arguments to each command.
+
+All commands up to the first space character may be entered in UPPER
+or lower case or MiXEd case. Qualifiers for commands (e.g. REL) must
+be written in UPPER case.
+
+Command Reference:
+
+\begin{verbatim}
+<int> = enter an integer (e.g. 240)
+<float> = enter a floating point number (e.g. 0.45)
+<string> = enter a string (e.g. ARNDql)
+<qstring> = enter a quoted string (e.g. "Active Site")
+<char> = enter a single character.
+\end{verbatim}
+
+\subsubsection{STEP 1 COMMANDS}
+
+These all refer to either system settings - e.g. the maximum allowed
+sequence length, or to general page layout features. e.g. the longest
+and shortest side of the paper on which you are plotting.
+
+\subsubsection{REQUIRED STEP 1 COMMANDS}
+
+BLOCK\_FILE\ $<$string$>$
+
+Gives the name of the file that contains the multiple sequence alignment
+to be formatted. File names should be fully qualified i.e. not
+relative to the current directory. If no block file command is given,
+ALSCRIPT will expect to read the block file from standard input.
+
+OUTPUT\_FILE\ $<$string$>$
+
+Defines the output file name. This command should be near the beginning of
+the command list.
+e.g. OUTPUT\_FILE\ Figure1.ps
+
+You MUST define an output file unless the -p option
+(See \hyperref{Alternative ways of invoking ALSCRIPT}{Section }{ }{app7})
+is used.
+
+DEFINE\_FONT\ $<$int$>$ $<$string$>$ ($<$int$>$/DEFAULT)/(REL $<$float$>$)
+
+Defines a font to use later:
+e.g.
+\begin{verbatim}
+DEFINE_FONT 0 Helvetica 10
+DEFINE_FONT 2 Times-Roman 2
+\end{verbatim}
+
+defines font number 0 to be 10 point Helvetica, and font number 2 to be
+2 point Times-Roman. Font 0 is always used as the default font. You MUST
+define at least the font 0 font.
+
+DEFINE\_FONT\ 3 Times-Roman DEFAULT
+
+sets font 3 to be Times-Roman at whatever the default pointsize
+is as set by the POINTSIZE command.
+
+DEFINE\_FONT\ 4 Helvetica REL 0.5
+
+sets font 4 to be helvetica at half the default pointsize.
+
+NOTE: Font names must be written exactly as shown in
+\hyperref{PostScript Fonts}{Section }{ }{app3}.
+
+
+SETUP
+
+Signals the end of the STEP 1 commands.
+
+\subsubsection{OPTIONAL STEP 1 COMMANDS}
+
+
+ADD\_SEQ\ $<$int$>$ $<$int$>$
+
+Allows extra sequence positions to be created in an existing alignment. This
+permits additional annotations to be interspaced either above, below, or
+anywhere in the middle of an alignment. For example:
+
+ADD\_SEQ\ 0 10
+
+would create an additional 10 sequences - all set to the blank character
+before the first sequence in the block file that has been read in.
+
+ADD\_SEQ\ 3 1
+
+would add an extra sequence after sequence 3.
+
+IMPORTANT: If you use the ADD\_SEQ\ facility to add sequences anywhere except
+after the last sequence, then remember that the sequence
+numbers will alter. All formatting commands that follow this command
+must use the new sequence numbering. Thus in the first example:
+
+ADD\_SEQ\ 0 10
+
+what was sequence number 1 becomes sequence 11. Sequences 1-10 are
+the new blank sequences to be used for annotation. Note that the
+sequence numbers only change for commands AFTER the SETUP command,
+thus, multiple add\_seq\ commands refer to the sequence number as
+implied by the block file.
+
+POINTSIZE $<$int$>$
+
+Defines the pointsize to be used to scale the plot and space the characters.
+Default is 10 point.
+
+NUMBER\_SEQS
+
+If present, then the sequence number is output with the identifier
+code. This is useful for finding the coordinates of residues to box
+or otherwise highlight.
+
+LANDSCAPE
+
+Specifies that alignments will be plotted with the longest paper axis
+horizontal. (Can get longer alignments on a page this way).
+
+PORTRAIT
+
+Specifies that alignments will be plotted with the longest paper axis vertical
+(can get more sequences on a page this way).
+
+IDENT\_WIDTH\ $<$int$>$
+
+Units are characters.
+
+Reserves $<$int$>$ characters at left of every page for plotting
+identifiers. Note that not all this space need be used, if a smaller
+pointsize is used to plot out the identifier codes, than is used for
+the main alignment.
+
+LINE\_WIDTH\_FACTOR\ $<$float$>$
+
+Value greater than 0 that scales the default line width. The linewidth
+is obtained by multiplying the pointsize by this factor.
+
+
+X\_SPACE\_FACTOR\ $<$float$>$
+
+Y\_SPACE\_FACTOR\ $<$float$>$
+
+This determines the spacing between adjacent residues in the X and Y
+directions. The spacing is calculated as: POINTSIZE + POINTSIZE *
+X\_SPACE\_FACTOR or POINTSIZE + POINTSIZE * Y\_SPACE\_FACTOR\ as
+appropriate. Defaults are 0.2 and 0.0 respectively.
+
+X\_SHIFT\_FACTOR\ $<$float$>$
+
+Y\_SHIFT\_FACTOR\ $<$float$>$
+
+These determine the shift relative to the residue drawing position
+that is given to the boxing lines. The shift is calculated as
+follows
+
+(POINTSIZE + POINTSIZE * X\_SPACE\_FACTOR)\ * X\_SHIFT\_FACTOR\
+similarly for Y\_SHIFT\_FACTOR.
+
+The defaults are 0.3 and 0.0 respectively.
+
+Fiddling with the X\_SPACE/SHIFT\ values is useful to fine tune the
+appearance of the alignment.
+
+
+MAX\_INPUT\_LEN\ $<$int$>$
+
+Units are characters.
+Defines the maximum number of characters possible in the input line
+length. This must be greater than the maximum number of sequences
+(MAX\_NSEQ).
+
+e.g. MAX\_INPUT\_LEN\ 600
+
+Increases the default value of 500 characters to 600 characters.
+
+MAX\_NSEQ\ $<$int$>$
+
+Units are characters. Defines the maximum number of sequences that
+may be read by the program. This parameter has a large default (500).
+You may need to reduce it on computers with small memories.
+
+MAX\_ILEN\ $<$int$>$
+
+Units are characters.
+The maximum length allowed for a sequence identifier code.
+
+MAX\_SEQ\_LEN\ $<$int$>$
+
+Defines the maximum length allowed for a sequence alignment - this may
+need to be reduced from the 8000 default value on smaller computers.
+
+X\_OFFSET\ $<$int$>$
+Units of points (1/72 inch).
+
+Defines the offset along the X-axis that the alignments will be shifted prior
+to printing. Fiddle with this value to get a nice offset from the bottom left
+hand corner of the page if your page size is not A4.
+
+Y\_OFFSET\ $<$int$>$
+Units of points (1/72 inch).
+
+As for X\_OFFSET,\ only Y axis.
+
+MAX\_SIDE\ $<$int$>$
+Units of inches.
+
+Defines the length of the longest side of the printer page.
+
+MIN\_SIDE\ $<$int$>$
+Units of inches.
+
+Defines the length of the shortest side of the printer page.
+
+VERTICAL\_SPACING\ $<$int$>$
+
+Defines the vertical spacing in character units between blocks of sequences
+when more than one block will fit on a page - default is 0.
+
+
+DEFINE\_COLOUR\ $<$int$>$ $<$float$>$ $<$float$>$ $<$float$>$
+
+DEFINE\_COLOR
+
+Defines a colour - the first number is a number by which the colour will
+be referred. The following three numbers are the intensities of red,
+green and blue respectively. Thus:
+
+DEFINE\_COLOUR\ 1 0 0.2 0.8
+
+sets colour number 1 to be a colour with no red, 0.2 green and 0.8 blue.
+The exact appearance of this colour will depend on the output device.
+If you find suitable combinations of colours for your printer, then
+please let me know and I shall distribute your suggestions with the
+program.
+
+DO\_TICKS
+
+If present, then tick marks are drawn below the numbers at the top of the page.
+Otherwise no ticks are shown.
+
+NUMBER\_INT\ $<$int$>$
+
+Specifies the interval for writing residue position numbers. Default is 10
+
+NO\_NUMBERS
+
+Switches all residue numbering off.
+
+
+\subsubsection{STEP 2 COMMANDS}
+
+
+All these are optional formatting commands.
+
+IMPORTANT PLEASE READ THIS NOTE:
+
+For those commands that accept region definitions (e.g. SURROUND\_CHARS) it
+is easiest to think of the region being defined in terms of X and Y
+coordinates, where X is the sequence residue coordinate and Y is the
+sequence number coordinate. Thus 3 7 means the 3rd residue in sequence 7.
+3 7 12 42 means the rectangular box bounded by residue 3 of sequence 7 and
+residue 12 of sequence 42.
+
+SURROUND\_CHARS\ $<$string$>$ ALL
+
+Draw lines round, but not between the characters that are in the string.
+e.g.
+
+SURROUND\_CHARS\ GP ALL
+
+will draw lines round all G and P characters in the alignment, but not
+between adjacent G and P characters.
+
+SURROUND\_CHARS\ $<$string$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$
+
+Similar command, but the surrounding is restricted to the region defined by
+the four integers.
+
+e.g.
+
+SURROUND\_CHARS\ ILVW 3 12 7 32
+
+would surround ILVW characters that occur in the region defined
+from residue positions 3-7 of sequences 12 to 32.
+
+SHADE\_CHARS\ $<$string$>$ ALL $<$float$>$
+
+Shade all characters in the $<$string$>$ by the grey value given by $<$float$>$.
+e.g.
+
+SHADE\_CHARS\ GP ALL 0.5
+
+would shade all G and P characters in the alignment by the grey value 0.5.
+
+SHADE\_CHARS\ $<$string$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$float$>$
+
+restricts the shading to the region defined by the four integers. Thus
+
+SHADE\_CHARS\ ILVW 3 12 7 32 0.7
+
+would shade I L V and W characters from residues 3-7 of sequences 12-32
+inclusive with a grey value of 0.7.
+
+FONT\_CHARS\ $<$string$>$ ALL $<$int$>$
+
+e.g.
+
+FONT\_CHARS\ GP ALL 7
+
+would use font 7 to write out all G and P characters. Font 7 MUST have been
+defined using the DEFINE\_FONT commands above.
+
+FONT\_CHARS\ $<$string$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$
+
+Similar to previous command, but restricts the effect to the region defined
+by the first four integers. The font must have been defined by the
+DEFINE\_FONT\ command.
+
+e.g.
+
+FONT\_CHARS\ ILVW 3 45 9 70 7
+
+Would set the font to 7 for I L V and W characters for residues 3-9 of
+sequences 45-70 inclusive. The font must have been defined by the
+DEFINE\_FONT\ command.
+
+FONT\_REGION\ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$
+
+Define the font to use throughout the region specified by the first four
+integers.
+
+e.g.
+
+FONT\_REGION\ 3 12 20 40 10
+
+Use font 10 for residues from residues 3-20 of sequences 12-40. The font
+must have been defined using the DEFINE\_FONT command.
+
+FONT\_RESIDUE\ $<$int$>$ $<$int$>$ $<$int$>$
+
+Set the font for use with a single residue position - most useful when used
+with the TEXT command.
+
+e.g.
+
+FONT\_RESIDUE\ 3 7 2
+
+Use font 2 for residue 3 of sequence 7. Font 2 must have been defined using
+the DEFINE\_FONT\ command.
+
+LINE $<$string$>$ $<$int$>$ $<$int$>$ $<$int$>$
+
+There are four commands of this type for drawing horizontal or vertical lines
+on the alignment.
+
+LINE LEFT $<$int$>$ $<$int$>$ $<$int$>$
+
+Draw a line to the left of the character positions indicated.
+
+e.g.
+
+LINE LEFT 3 12 24
+
+Draw a vertical line starting at residue 3 of sequence 12 and ending at
+residue 3 of sequence 24.
+
+LINE TOP 3 12 24
+
+Draw a horizontal line above the character positions from residue 3 of
+sequence 12 to residue 24 of sequence 12.
+
+Similar commands are:
+
+LINE BOTTOM $<$int$>$ $<$int$>$ $<$int$>$ Draw a line at bottom of character position.
+
+LINE RIGHT $<$int$>$ $<$int$>$ $<$int$>$ Draw a line at right of character position.
+
+BOX\_REGION\ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$
+
+Draw a box around the region indicated by the four integers.
+
+e.g.
+
+BOX\_REGION\ 2 5 30 7
+
+Would box from residue 2 of sequence 5 to residue 30 of sequence 7.
+
+SHADE\_REGION\ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$float$>$
+
+Shade the region indicated by the integers with the grey value shown by the
+float.
+e.g.
+
+SHADE\_REGION\ 30 40 35 46 0.2
+
+Would shade from residue 30-35 of sequences 40-46 with a grey value of 0.2.
+
+SHADE\_RES\ $<$int$>$ $<$int$>$ $<$float$>$
+
+Shade just one amino acid with the grey value.
+
+e.g.
+
+SHADE\_RES\ 3 4 0.7
+
+Shades residue 3 of sequence 7. (Note: this can also be achieved with the
+
+SHADE\_REGION\ command, but requires 2 extra numbers)
+
+TEXT $<$int$>$ $<$int$>$ $<$qstring$>$
+
+Place the text string at the location indicated.
+
+e.g.
+
+TEXT 30 70 "Active Site His"
+
+would put the text Active Site His starting at position 30 of sequence
+70. (Use FONT\_RESIDUE\ or FONT\_REGION\ commands to set the font of the
+text). Text added with the TEXT command will not be split across page
+breaks, so you may in some circumstances need to fiddle a little with
+the location/pointsize for the text to get the desired result.
+
+ID\_FONT\ ALL $<$int$>$
+
+Set the font for all identifier codes to the font number shown by $<$int$>$.
+e.g.
+
+ID\_FONT\ ALL 3
+
+Would set all the identifier codes to font 3.
+
+ID\_FONT\ $<$int$>$ $<$int$>$
+
+Set the font for a specific identifier to font number.
+e.g.
+
+ID\_FONT\ 12 4
+
+Use font 4 for the identifer of sequence 12, default font for all other
+identifiers.
+
+SUB\_CHARS\ ALL $<$char$>$ $<$char$>$
+
+Substitute the characters indicated.
+
+e.g.
+
+SUB\_CHARS\ ALL + *
+
+would change all occurences of + to * in the alignment.
+
+SUB\_CHARS\ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$char$>$ $<$char$>$
+
+restrict the substitution to the region shown.
+
+e.g.
+
+SUB\_CHARS\ 1 1 7 8 \% *
+
+would substitute * for \% from residue 1-7 of sequences 1-8.
+NOTE: To substitute for or with the space character use the word SPACE.
+e.g. to change all space characters to -.
+
+SUB\_CHARS\ ALL SPACE -
+
+SUB\_ID\ $<$int$>$ $<$qstring$>$
+
+Replace the numbered identifier by the string.
+e.g.
+
+SUB\_ID\ 34 "Predicted Secondary Structure"
+
+would replace whatever the identifier of sequence 34 was, by the text shown.
+This is useful when used in conjunction with the ADD\_SEQ\ command shown under
+the STEP 1 commands.
+
+INVERSE\_CHARS\ $<$string$>$ ALL/Range (similar syntax to FONT\_CHARS\ but no
+font number)
+
+Print the selected characters in white. This clearly will only work
+if you first use the SHADE\_CHARS command to shade the characters with
+something other than white.
+
+CCOL\_CHARS\ $<$string$>$ ALL $<$int$>$
+
+Colour all characters in the $<$string$>$ by the colour defined by $<$int$>$.
+
+e.g.
+
+CCOL\_CHARS\ GP ALL 12
+
+would colour all G and P characters in the alignment by the colour 12.
+This colour MUST have been defined by the DEFINE\_COLOUR\ command.
+
+CCOL\_CHARS\ $<$string$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$
+
+restricts the colouring to the region defined by the four integers. Thus
+
+CCOL\_CHARS\ ILVW 3 12 7 32 7
+
+would colour I L V and W characters from residues 3-7 of sequences 12-32
+inclusive with the colour 7.
+
+SCOL\_CHARS:\ This has identical syntax to SCOL\_CHARS,\ but colours the
+background of the character, rather than the letter itself.
+
+COLOUR\_REGION\ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$ $<$int$>$
+
+COLOR\_REGION
+
+Colour the region indicated by the integers with the colour number given
+as the last number.
+
+e.g.
+
+COLOUR\_REGION\ 30 40 35 46 2
+
+Would colour from residue 30-35 of sequences 40-46 with the colour 2.
+
+COLOUR\_RES\ $<$int$>$ $<$int$>$ $<$int$>$
+
+Colour just one amino acid with the defined colour.
+
+e.g.
+
+COLOUR\_RES\ 3 4 7
+
+Colours residue 3 of sequence 7. (Note: this can also be achieved with the
+COLOUR\_REGION\ command, but requires 2 extra numbers)
+
+
+\subsection{AMPS Block file format}
+\label{app2}
+
+The first part of a block-file contains the identifier codes of the
+sequences that are to follow. Each code is prefixed by the $>$ symbol, codes
+must not contain spaces.
+
+e.g.
+\begin{verbatim}
+>HAHU
+>Trypsin
+>A0046
+>Seq1
+
+\end{verbatim}
+
+etc.
+
+ALSCRIPT counts the number of $>$ symbols in the beginning of the file
+until a * symbol is found. The * signals the beginning of the
+multiple alignment which is stored VERTICALLY, thus columns are
+individual sequences, whilst rows are aligned positions. The * symbol
+must lie over the first sequence. A further star in the same column
+signals the end of the alignment. ALSCRIPT uses the number of $>$
+symbols at the beginning of the file to work out how many columns to
+read from the * position. It is therefore important that the only $>$
+symbols in the file are those that define the identifiers, and the
+only * symbols are those defining the start and end of the multiple
+alignment. The block file can contain additional text, providing that
+there are no more $>$ or * symbols in the file than those used to define
+the identifiers or alignment start and end.
+
+A simple, small block-file is shown here.
+
+\begin{verbatim}
+>Seq_1
+>A0231
+>HAHU
+>Four_Alpha
+>Globin
+>GLobin_C
+*
+ARNDLQ
+AAAAAA
+PPPPPP
+PP PPP
+WW WWW
+LLLLLL
+IIVVLL
+*
+\end{verbatim}
+
+
+\subsection{PostScript Fonts}
+\label{app3}
+\begin{verbatim}
+Times-Roman,
+Times-Italic,
+Times-Bold,
+Times-BoldItalic,
+Helvetica,
+Helvetica-Oblique,
+Helvetica-Bold,
+Helvetica-BoldOblique,
+Courier,
+Courier-Oblique,
+Courier-Bold
+Courier-BoldOblique,
+AvantGarde-Book,
+AvantGarde-BookOblique,
+AvantGarde-Demi,
+AvantGarde-DemiOblique,
+Bookman-Demi,
+Bookman-DemiItalic,
+Bookman-Light,
+Bookman-LightItalic,
+Helvetica-Narrow,
+Helvetica-Narrow-Bold,
+Helvetica-Narrow-BoldOblique,
+Helvetica-Narrow-Oblique,
+NewCenturySchblk-Roman,
+NewCenturySchlbk-Bold,
+NewCenturySchblk-Italic,
+NewCenturySchblk-BoldItalic,
+Palatino-Roman,
+Palatino-Bold,
+Palatino-Italic,
+Palatino-BoldItalic
+ZapfChancery-MediumItalic.
+Symbol
+\end{verbatim}
+
+\subsection{386 DOS installation}
+\label{app4}
+
+
+IMPORTANT - The programs on this disk will ONLY WORK on a PC with a 386
+or better processor. See the Technical Notes section for details of why.
+
+Directions:
+
+\begin{enumerate}
+
+\item
+ Create a directory on your hard disk.
+ e.g. mkdir ALSCRIPT.
+
+\item
+ Copy the Contents of the floppy disk into this directory.
+\begin{verbatim}
+ e.g. copy a:*.* c:\alscript.
+\end{verbatim}
+
+\item
+ Edit your AUTOEXEC.BAT file and add
+\begin{verbatim}
+ C:\ALSCRIPT to your path.
+\end{verbatim}
+
+\item
+ Edit your AUTOEXEC.BAT file and add the following two lines.
+ set DOS4GVM=@ALSCRIPT.VMC
+ set DOS4G=quiet
+\end{enumerate}
+
+The first line is an instruction to read instructions from the file
+ALSCRIPT.VMC. This sets up a permanent swap file on your hard disk.
+By default, the swap file is about 12MBytes in size. If you do not have
+this much free space on your disk, then edit the ALSCRIPT.VMC file
+to reduce the swap file size, or alternatively, do not put this line
+in your autoexec.bat.
+
+The programs will run without this swap file, but you will be limited in
+ the size of alignment you can process by the amount of RAM you have
+installed. I have only tested this program on a 486/33 with 8MBytes RAM
+and a 386/33 with 4MBytes so I do not know the practical limitations of
+machines with smaller memories. Any feedback would be appreciated.
+
+5. Type AUTOEXEC.BAT to initialise the changes, or better still, reset
+the computer.
+
+6. You should now be able to run all three programs in the package from
+anywhere on your disk. msf2blc, clus2blc and alscript. If you get
+memory allocation errors when you try to run alscript, then use the
+MAX\_NSEQ\ and MAX\_SEQ\_LEN\ commands to reduce the default limits. If the
+program still won't run, then think about buying some more memory!!
+
+The programs msf2blc and clus2blc should run OK, but if you try to
+process alignments that are too large for your computer, you may get a
+"malloc error" which will stop the program. If this happens and you are
+not using the virtual memory option discussed above, then try adding the
+line set DOS4GVM=@filename to your autoexec.bat file. If you
+don't have enough disk space to do this, then buy a bigger disk, or more
+memory.
+
+\subsection{TECHNICAL NOTES}
+
+The executables included in this package were compiled with the WATCOM C
+compiler. This is a full 32 bit compiler that makes good use of the 386
+processor and does not work on the 16 bit 286. It also has the
+advantage of allowing the flat memory model to be used. In practice
+this means that porting programs like alscript from Unix computers like
+the Sun, is straightforward. In order to access the memory of the
+computer in this way, an extra program called a dos extender is required
+- this is called DOS4GW.EXE. DOS4GW is automatically invoked every time
+you run one of the programs and is responsible for managing the memory and
+creating the swap file discussed above.
+
+\subsection{Unix Installation}
+\label{app5}
+
+ALSCRIPT is distributed with executables for Sun (SunOS 4.1.3), Silicon
+Graphics (IRIX 5.3), DEC ALPHA OSF/1 and Sun Solaris (2.4). The executables
+are stored in the subdirectories bin/sun, bin/sgi, bin/osf and bin/sol. If
+these are OK for your system, then just add the apporpriate directory to your
+path, or put links to /usr/local/bin or somewhere that is on all users paths.
+
+The source code for ALSCRIPT is contained in a directory hierarchy.
+The top directory contains a README file and the BUILD script.
+Subdirectories are: {\bf examples} which contains example command and
+alignment files, {\bf doc} which contains \LaTeX and PostScript copies
+of the manual - a subdirectory of this contains an HTML version of the
+manual, and {\bf src} which contains the source code and Makefiles for
+the package. There may also be a directory called {\bf bin}. If
+present this will contain subdirectories with executables for the
+programs in the package. Makefiles to build alscript, msf2blc,
+clus2blc and alsnum are included in the {\bf src} directory. Versions
+for Sun (acc compiler .sun), Silicon Graphics (.sgi), DEC OSF/1 (.osf)
+are included.
+
+There is a utility csh script called BUILD. Simply type ./BUILD sun to
+compile alscript on the Sun, ./BUILD sgi for Silicon Graphics or BUILD
+gcc for use with gcc compiler. See instructions in the file BUILD.
+The BUILD script will create a /bin directory and subdirecotry
+if not already present. You can create makefiles for different computers
+and the BUILD script should still function.
+
+
+\subsection{VAX/VMS Installation}
+\label{app6}
+
+The standard VAX C compiler is not ANSI. Accordingly, ALSCRIPT will require
+changes to the source code to compile on a VAX.
+
+The DEC C++ compiler works OK for alscript. Alscript will also compile
+on Dec ALPHA under OpenVMS. A descrip.mms file is included for this
+purpose.
+
+{\em WARNING: I've not tested Version 2.0 of ALSCRIPT on VMS}
+
+\subsection{Alternative ways of invoking ALSCRIPT}
+\label{app7}
+
+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.
+
+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".
+
+Ways of running alscript:
+
+\begin{enumerate}
+
+\item
+ 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.
+
+\item
+ alscript $<$command\_file$>$\ has same effect as 1, But does not prompt for
+ the command file
+ e.g. alscript example1.als
+
+\item
+ 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.
+
+ e.g. alscript -q $<$ example1.blc $>$ example1.ps
+
+\item
+ alscript -f $<$command\_file$>$
+ Similar effect to 2.
+
+\item
+ 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.
+
+\item
+ 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
+
+ e.g. alscript -f example1.als -p -s $<$ example1.blc $>$ example1.ps
+
+\end{enumerate}
+
+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:
+
+msf2blc -q $<$pileup.msf | alscript -q -s | lpr
+
+\subsection{Program Crashes and Known Bugs}
+\label{app8}
+
+We've used ALSCRIPT on Sun Workstations and Silicon Graphics for some
+time, with very large alignments and command files with thousands of
+commands. All seems to work OK, the program has not crashed on us at
+all!!
+
+However, the command interpreter in ALSCRIPT is very simple and
+the program will crash if you give any command the wrong number of
+arguments (e.g. leaving out the shade value in a shade\_chars\ command).
+
+If you do make the program crash, have checked all the documentation
+and your numbers, and the program still crashes. Then send me
+the command file and block file that causes the crash and I will try
+to investigate.
+
+Suggestions for improvements to the program are always welcome.
+
+\subsection{Wish List for next version!!}
+\label{app9}
+
+A command interpreter that does more error checking will be included.
+Currently, no checking is done to make sure that the correct number of
+arguments are given to a command.
+
+Sequences will be able to be given unique labels and region commands refer
+to these labels or ranges of labels. This will permit a sequence to be
+deleted or added to the alignment without having to update the .als file.
+
+The relative numbering option will be extended to allow numbering relative
+to a position. e.g. 456+7 would be 7 residues after position 456. This
+will allow annotation of positions that may be in insertions relative to the
+reference sequence.
+
+Special TEXT commands will be extended to allow alternative shapes to
+be drawn and scaled in various ways.
+
+Tree drawing and generalised graphics. An option to draw arbitrary lines
+on an alignment will be added. This will permit line graphics to be added
+to an alignment. The initial reason for this will be to show dendrograms
+(trees) alongside the alignment, but simple line graphs could also be plotted
+under the alignment.
+
+Fiddle factors will be introduced to allow fine positioning of
+individual characters. For example, if you like your ``I'' characters
+to be centred rather than left justified, this will be possible.
+
+In single\_page mode, it will be possible to add arbitrary text to an
+alignment for final annotation, e.g. titles etc.
+
+Variable height/width sequence lines will be permitted (maybe).
+
+\subsection{Acknowledgements}
+
+I thank all those who have emailed me with suggestions for
+improvements to alscript. I've tried to include some of these in the
+current distribution (e.g. screening).
+
+\subsection{References}
+\label{app10}
+
+\begin{verbatim}
+
+1. Barton, G. J. (1993),
+ "ALSCRIPT A tool to format multiple sequence alignments",
+ Protein Engineering, Volume 6, No. 1, pp.37-40.
+
+2. Barton, G. J. (1990),
+ "Protein Multiple Sequence Alignment and Flexible Pattern Matching",
+ Methods in Enzymology,
+ 183,403-428.
+
+3. Barton, G. J. and Sternberg, M. J. E. (1987),
+ "A Strategy for the Rapid Multiple Alignment of Protein Sequences:
+ Confidence Levels From Tertiary Structure Comparisons",
+ Journal of Molecular Biology,
+ 198,327-337
+
+4. Higgins, D. G. and Sharp, P. M. (1989),
+ "Fast and sensitive multiple sequence alignments on a microcomputer",
+ CABIOS,
+ 5,151--153
+
+5. Devereux, J. Haeberli, P. Smithies, O. (1984),
+ "A comprehensive set of sequence analysis programs for the VAX",
+ Nucleic Acids Res.
+ 12, 387-395
+
+6. Livingstone, C. D. and Barton, G. J. (1993),
+ "Protein Sequence Alignments: A Strategy for the Hierarchical analysis
+ of residue conservation"
+ Computer Applications in the Biosciences,
+ 9, 745-756.
+
+\end{verbatim}
+\end{document}
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git://source.jalview.org / jpred.git / blobdiff