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ali2gff(1) [debian man page]

ALI2GFF(1)						      General Commands Manual							ALI2GFF(1)

NAME
ali2gff - Module to translate a MUMmer output files into gff formatted output. SYNOPSIS
ali2gff [-r] [-t <.|0|1|2>] [-x <name>] [-y <name>] [-H] [-f] [-h] <MUMmer_output_file> OPTIONS
-h, --help Show summary of options. -r Interchange the order of sequences (sequence 1 on y-axis, sequence 2 on x-axis). -t <.|0|1|2> Put label 'frame' in gff output. -x <name> Specify the species name for species1 (default: "Seq1"). -y <name> Specify the species name for species2 (default: "Seq2"). -i Ignore full sequence identities. -f Write output to file. SEE ALSO
blat2gff(1), gff2aplot(1), parseblast(1), sim2gff(1). AUTHOR
ali2gff was written by Steffi Gebauer-Jung. 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 ALI2GFF(1)

Check Out this Related 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)

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