sim2gff(1) [debian man page]

SIM2GFF(1)						      General Commands Manual							SIM2GFF(1)

NAME

       sim2gff - Converts SIM file into GFF formatted records

SYNOPSIS

       sim2gff [-frxyHh] sim_file > gff_file

DESCRIPTION

       This manual page documents briefly the sim2gff command.

       sim2gff is a program written in Perl that converts SIM file into GFF formatted records (for use with gff2aplot and gff2javaplot).

OPTIONS

       -h, --help
	      Show summary of options.

       -f     Output is written to a file named <sim_file>.gff.

       -r     Interchange the order of sequences (Seq1 on y-axis, Seq2 on x-axis).

       -x <name>
	      Specify the species name for species1 (default: "Seq1").

       -y <name>
	      Specify the species name for species2 (default: "Seq2").

       -H     Use the fasta file headers for species labels.

EXIT STATUS

       The following perl-like exit status are returned:

       0 Error

       1 Successful completion

SEE ALSO

       ali2gff(1), blat2gff(1), gff2aplot(1), parseblast(1).

AUTHOR

       sim2gff was written by Thomas Wiehe <twiehe@imb-jena.de>.

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others).

							  Mon, 21 Mar 2005 21:44:15 -0300						SIM2GFF(1)

SEQSPLIT(1)						      General Commands Manual						       SEQSPLIT(1)

NAME

       seqsplit - split seqs into chunks of defined size and overlap

SYNOPSIS

       seqsplit [-options] <seqfile>

DESCRIPTION

       This manual page documents briefly the seqsplit command.

       seqsplit is a program that splits sequences into smaller chunks of defined size and overlap; output a FASTA file.

OPTIONS

       -h     Help; display usage and version.

       -o <file>
	      Output the new FASTA file to <file>.

       --fragfile <f>
	      Save one-line-per-frag coord summary file to <f>.

       --informat <s>
	      Specify sequence file format <s>.

       --length <n>
	      Set max length of each unique seq frag to <n>.

       --overlap <n>
	      Set overlap length to <n> (total frag size = length+overlap).

       --shortnames
	      Use short "frag1" names, not "<src>/<from>-<to>".

LIMITATIONS

       Still working in 32 bits -- no sequence can be more than 2 GB in size.

SEE ALSO

       afetch(1),  alistat(1), compalign(1), compstruct(1), revcomp(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1),
       weight(1).

AUTHOR

       Sean Eddy
       HHMI/Department of Genetics
       Washington University School of Medicine
       4444 Forest Park Blvd., Box 8510
       St Louis, MO 63108 USA
       Phone: 1-314-362-7666
       FAX  : 1-314-362-2157
       Email: eddy@genetics.wustl.edu

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
       for the Debian project (but may be used by others).

							  Mon, 01 Aug 2005 15:28:08 -0300					       SEQSPLIT(1)