Tophylip

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TOPHYLIP

FUNCTION

ToPhylip writes GCG sequences into a single file in Phylip format.

DESCRIPTION

ToPhylip converts a set of sequences grom GCG to Phylip format, ready for use in Joe Felsenstein's program Phylip.

AUTHOR

This program was written by Jack A.M. Leunissen (E-mail: jackl@caos.kun.nl; Post: CAOS/CAMM Center, University of Nijmegen, 6525 ED Nijmegen, The Netherlands).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a sample session with ToPhylip 

  
  
  % tophylip
  
   TOPHYLIP uses any sequences
  
   TOPHYLIP of what sequence(s) ?  @pretty.list
  
                   fa10.ugly, len: 349
                   fa12.ugly, len: 349
                   fo1k.ugly, len: 349
                      e.ugly, len: 349
                    p1m.ugly, len: 349
                    p1s.ugly, len: 349
                    p2s.ugly, len: 349
                    p3s.ugly, len: 349
                    cb3.ugly, len: 349
                    r14.ugly, len: 349
                     r2.ugly, len: 349
  
               Start (* 1 *) ?
             End (*   349 *) ?
  
   What should I call the output file (* pretty.phylip *) ?
  
  %

OUTPUT

The output from ToPhylip is a phylip formated sequence(s) file.

Here is the output file from the above example. 

  
  
   1 380
  fos_human   MMFSGFNADY EASSSRCSSA SPAGDSLSYY HSPADSFSSM GSPVNAQDFC
  
         TDLAVSSANF IPTVTAISTS PDLQWLVQPA LVSSVAPSQT RAPHPFGVPA
  
         PSAGAYSRAG VVKTMTGGRA QSIGRRGKVE QLSPEEEEKR RIRRERNKMA
  
         AAKCRNRRRE LTDTLQAETD QLEDEKSALQ TEIANLLKEK EKLEFILAAH
  
         RPACKIPDDL GFPEEMSVAS LDLTGGLPEV ATPESEEAFT LPLLNDPEPK
  
         PSVEPVKSIS SMELKTEPFD DFLFPASSRP SGSETARSVP DMDLSGSFYA
  
         ADWEPLHSGS LGMGPMATEL EPLCTPVVTC TPSCTAYTSS FVFTYPEADS
  
         FPSCAAAHRK GSSSNEPSSD SLSSPTLLAL

INPUT FILE

The input file for ToPhylip is a GCG sequence file.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide. 

  
  
  Syntax: % tophylip [-INfile=]@pretty.list -Default
  
  Required Parameters:
  
  -BEGin=1 -END=349        range of interest
  [-OUTfile=]pretty.phylip  output file
  
  Local Data Files:
  
  None
  
  Optional Parameters:
  
  -LINesize=50       sets the number of residues per line
  -BLOcksize=10      sets the number of residues per block

LOCAL DATA FILES

The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

Printed: April 22, 1996 15:56 (1162)