gcg2 21% pretty fetch.msf{*}

Pretty displays multiple sequence alignments and calculates a
consensus sequence.  It does not create the alignment; it simply
displays it.

          fetch.msf{capb_chick}  len: 278  wgt: 1.00
          fetch.msf{capb_mouse}  len: 278  wgt: 1.00
          fetch.msf{capb_human}  len: 278  wgt: 1.00
          fetch.msf{capb_caeel}  len: 278  wgt: 1.00

                  Begin (* 1 *) ?
                End (*   278 *) ?

 What should I call the output file (* pretty.pretty *) ?  fetch.pretty

gcg2 22% cat fetch.pretty
PRETTY of: fetch.msf{*}   March 24, 2000 01:31  ..

                       1                                                   50
fetch.msf{capb_chick}  MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA
fetch.msf{capb_mouse}  MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA
fetch.msf{capb_human}  MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA
fetch.msf{capb_caeel}  MGEQQLDCAL DLMRRLPPQH CDKNLTDLID LCPHLVDDLL STIDQPLKIA

                       51                                                 100
fetch.msf{capb_chick}  RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA
fetch.msf{capb_mouse}  RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA
fetch.msf{capb_human}  RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA
fetch.msf{capb_caeel}  ADRETGKQYL LCDYNRDGDS YRSPWSNTYD PPLEDGQLPS EKRRKMEIEA

                       101                                                150
fetch.msf{capb_chick}  NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD
fetch.msf{capb_mouse}  NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD
fetch.msf{capb_human}  NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD
fetch.msf{capb_caeel}  NAAFESYRDL YFEGGVSSVY FWDLDNGGFA GIVLIKKEGD GAKNITGCWD

                       151                                                200
fetch.msf{capb_chick}  SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKTGSGTMNL GGSLTRQMEK
fetch.msf{capb_mouse}  SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK
fetch.msf{capb_human}  SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK
fetch.msf{capb_caeel}  SIHVIEITER A..RQAHYKL TSTIMLWLQT NKSSSGVMNL GGSLTRQHEM

                       201                                                250
fetch.msf{capb_chick}  DETVSDSSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSIDAI
fetch.msf{capb_mouse}  DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSLDAI
fetch.msf{capb_human}  DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSVQTF
fetch.msf{capb_caeel}  DAPINDQNTH LANMGRMIED QESKMRLTIN EIYFGKTKKV MSDLRSTEKQ

                       251                        278
fetch.msf{capb_chick}  PDNQKYKQLQ RELSQVLTQR QIYIQPDN
fetch.msf{capb_mouse}  PDNHKFKQLQ RELSQVLTQR QVYIQPDN
fetch.msf{capb_human}  ADKSKQEALK NDLVEALKRK QQC~~~~~
fetch.msf{capb_caeel}  SELEKQDEIV RELNNAMANR GN~~~~~~

gcg2 23% prettybox fetch.pretty

PrettyBox displays  multiple sequence alignments in PostScript format,
using shading to represent regions that agree with a calculated
consensus sequence.  The program does not create the alignment;
it simply displays it.

PRETTYBOX what sequences ? fetch.msf{*}

         fetch.msf{capb_chick}, len: 278
         fetch.msf{capb_mouse}, len: 278
         fetch.msf{capb_human}, len: 278
         fetch.msf{capb_caeel}, len: 278


                  Begin (* 1 *) ?
                End (*   278 *) ?

Print in which orientation:

     l)andscape     p)ortrait

Please select (* L *):

Display a consensus (* No *) ? y

 Find consensus to what minimum plurality (* 2.00 *) ?

Where should numbers be placed:

     r)ight side     t)op      n)one

Please select (* R *):

What should I call the output PostScript file (* prettybox.ps *) ?  fetch.ps

gcg2 25% ls
best.pair             capb_mouse.sw         k02938.gb_ov
capb.txt              fetch.msf             list.msf
capb_caeel.swissprot  fetch.pretty          pileup.figure
capb_chick.sw         fetch.ps              pretty.pretty
capb_human.sw         gap.pair              x15785.gb_ov
gcg2 26%