ToPhylip writes GCG sequences into a single file in Phylip format.
ToPhylip converts a set of sequences grom GCG to Phylip format, ready for use in Joe Felsenstein's program Phylip.
This program was written by Jack A.M. Leunissen (E-mail: firstname.lastname@example.org; 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 (email@example.com).
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 *) ? %
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
The input file for ToPhylip is a GCG sequence file.
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
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.
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)