Augustus

• aln2wig(1) convert alignments to wig files
• augustus(1) a gene prediction tool
• bam2hints(1) convert mRNA-to-genome alignments in BAM format into a hint file for AUGUSTUS
• bam2wig(1) Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS.
• compileSpliceCands(1) Find introns parsing a set of exon candidates in GFF format
• etraining(1) train AUGUSTUS models
• fastBlockSearch(1) search loci matching protein block profiles
• filterBam(1) filter BAM file for use with AUGUSTUS tools
• getSeq(1) print genome sequences from databases on the standard output
• homGeneMapping(1) create summary of gene homology
• joingenes(1) merge several gene sets into one
• load2db(1) load genome sequences and extrinsic evidence hints into a MySQL database
• load2sqlitedb(1) load genome sequences and extrinsic evidence hints into a SQLite database
• pp_simScore(1) print similarity and alignments for block-profile and protein sequence on the standard output
• prepareAlign(1) prepare an alignment for block profile creation by deleting gap-rich rows