debian man page for ali2gff

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)