axt2phy.pl - convert AXT pairwise alignment files to GFF, Fasta and wig files
% axt2phy.pl -species speciesname -axtin AXTinputfile
This program reads an AXT pairwise alignment file and creates the GFF, Fasta and binary wig files to be used for the phylogenetic glyph for the Generic Genome Browser.
AXT alignment files are used by UCSC Genome Broser. A description of the AXT files can be found at:
The GFF entries make use of the GFF3 CIGAR format which creates gap entries as specified by:
-species Name or label of aligning species -axtin Filename of axt file
-fa_width Width of Fasta entries Default = 80 wigpath Path of output wig file Default = "." wigout Output wig file Default = axtin_<timestamp>.wig gffout Output GFF file Default = axtin_<timestamp>.gff fastaout Output Fasta file Default = axtin_<timestamp>.fa append Option to append GFF and Fasta entries to file Default = 0 start Minimum coordinate for entries to be considered Default = 0 stop Maximum coordinate for entries to be considered Default = 0 (off) chr Chromosome of reference sequences to be considered Default = "" (off)
Many options have aliases and can be abbreviated.
Bio::Graphics::Wiggle, Bio::Graphics::Glyph::phylo_align, Bio::Graphics::Glyph::wiggle_xyplot, Bio::Graphics::Glyph::wiggle_density, Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Feature, Bio::Graphics::FeatureFile
H. Mark Okada <email@example.com>.
Copyright (c) 2008
This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.