bp_aacomp(1p) [debian man page]

BP_AACOMP(1p)						User Contributed Perl Documentation					     BP_AACOMP(1p)

NAME

       aacomp - amino acid composition of protein sequences

SYNOPSIS

	 aacomp [-f/--format FORMAT] [-h/--help] filename
	 or
	 aacomp [-f/--format FORMAT] < filename
	 or
	 aacomp [-f/--format FORMAT] -i filename

DESCRIPTION

       This scripts prints out the count of amino acids over all protein sequences from the input file.

OPTIONS

       The default sequence format is fasta.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    aacomp filename

       named argument
	    aacomp -i filename

       standard input
	    aacomp < filename

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       Based on aacomp.c from an old version of EMBOSS

perl v5.14.2							    2012-03-02							     BP_AACOMP(1p)

BP_CHAOS_PLOT(1p)					User Contributed Perl Documentation					 BP_CHAOS_PLOT(1p)

NAME

       chaos_plot - a chaos plot from DNA and RNA sequences

SYNOPSIS

	 chaos_plot.pl -i/--input=INPUTFILE -f/--format=SEQFORMAT
	       -o/--output=OUTPUTFILE -g/--graphics=GRAPHIC FORMAT
	       -w/--width=WIGHT -h/--height=HEIGHT

DESCRIPTION

       This scripts generates image files using GD image library to visualize nucleotide sequences using chaos plot.

OPTIONS

       Valid graphics formats are currently gd, gd2, png, wbmp, jpeg and gif.

       The default size of the image file is 600x400.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    chaos_plot filename

       named argument
	    chaos_plot -i filename

       standard input
	    chaos_plot < filename

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       This code is based on EMBOSS C code for chaos.c by Ian Longden.	Included are documentation from EMBOSS code:

       Chaos produces a chaos plot.  The original application is part of the ACEDB genome database package, written by ** Richard Durbin (MRC LMB,
       UK) rd@mrc-lmba.cam.ac.uk, and Jean Thierry-Mieg (CRBM du CNRS, France) mieg@crbm1.cnusc.fr

perl v5.14.2							    2012-03-02							 BP_CHAOS_PLOT(1p)