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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)

Check Out this Related Man Page

WEIGHT(1)						      General Commands Manual							 WEIGHT(1)

NAME
weight - calculates sequence weights for an alignment SYNOPSIS
weight [-options] <alignment file> DESCRIPTION
This manual page documents briefly the weight command. weight is a program that calculates weights for a sequence alignment. OPTIONS
Available options: -b <f> Use BLOSUM weighting scheme at <f> fractional identity. -f <f> Filter out seqs w/ fractional ident > <x> [0-1]. -h Help; print version and usage info. -o <file> Save weight-annotated alignment in <outfile>. -p Use position based weight scheme (Henikoff & Henikoff). -s <n> Sample <n> sequences at random into a new alignment. -v Use Voronoi weight scheme (Sibbald & Argos). --informat <s> Specify alignment file format <s>. Allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP. --quiet Suppress verbose banner. SEE ALSO
afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(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 WEIGHT(1)

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