Here are some helpful notes on converting a mase IG alignment file to a publication quality boxed alignment.

These notes describe how to convert a mase IG file to a format that the
GCG pretty program, and the EGCG prettyplot/prettybox programs can read
to create publication quality alignments.

In the following example the mase file is called "inter4-SB.mase".  Please
note that if you used the new alignment program known as "pimaII" you will
have to convert your alignment file from table to IG format first
as follows:
cyrus%  tbl-to-IG inter4.align > inter4.mase <Return>

cyrus%  mkdir gcgtest <Return>
cyrus%  cp inter4-SB.mase gcgtest <Return>
cyrus%  cd gcgtest <Return>
~/medtest/inter4/gcgtest

(Now, change "-" to "." in the mase file because the gcg programs use
	a "." for a gap character instead of a "-". )
	cyrus%   sed 's/-/./g' inter-SB.mase > new.mase <Return>

cyrus%   <Return>
cyrus%  fromig new.mase <Return>
(The fromig command is a GCG command that converts IG files to gcg format.)
If you get the message:       "fromig: Command not found." it means that
you must be in gcg to use the fromig command.  Start up GCG as follows:)


cyrus%  gcg <Return>
cyrus%  fromig new.mase <Return>

cyrus%  dir <Return>
total 11
   1 1bbn3.                1 il4_pig.              1 inter4-sb23.
   1 1itl23.               2 inter4-SB.mase        1 inter4-sb3.
   1 1rcb123.              1 inter4-sb.
   1 il4_human123.         1 inter4-sb123.
cyrus%  delete inter4-sb*	 <Return>
(To delete all files that begin with the pattern name inter4-sb  )

cyrus%  pretty -con -case *. <Return>
(To create text file pretty.pretty.  The boxed file is created with the
prettyplot command below.  Your text output file will be saved in the
file pretty.pretty.)

cyrus%  egcg  <Return>
               extensions to GCG (EGCG)  initialized.

cyrus%  prettyplot -con -case -shortname *. <Return>
(In the above command "*." refers to all files that end with a ".",
which is all the gcg files.)

(Your boxed output file will be sent to the default system printer.)
(On cyrus this is the 	qms  printer.)

Note:
If you would like to change the default gcg graphical output device form
the system printer (qms or lj3a) to another printer such as "lj", or to
a postscript file, you can use the "postscript" command in GCG as follows:

cyrus% postscript <Return>
        Please choose one ( * LN03-SCRIPTPRINTER * )  <Return>
        To what port LN03-SCRIPTPRINTER connected (* |lpr -Pqms *) |lpr -Plj <Return>

or      To what port LN03-SCRIPTPRINTER connected (* |lpr -Pqms *) post.ps <Return>