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/usr/bin/aln2wig
/usr/bin/augustus
/usr/bin/bam2hints
/usr/bin/bam2wig
/usr/bin/checkTargetSortedness
/usr/bin/compileSpliceCands
/usr/bin/etraining
/usr/bin/fastBlockSearch
/usr/bin/filterBam
/usr/bin/homGeneMapping
/usr/bin/joingenes
/usr/bin/prepareAlign
/usr/share/augustus/scripts/README.autoAug
/usr/share/augustus/scripts/SplicedAlignment.pm
/usr/share/augustus/scripts/aa2nonred.pl
/usr/share/augustus/scripts/augustus2browser.pl
/usr/share/augustus/scripts/augustus2gbrowse.pl
/usr/share/augustus/scripts/autoAug.pl
/usr/share/augustus/scripts/autoAugPred.pl
/usr/share/augustus/scripts/autoAugTrain.pl
/usr/share/augustus/scripts/autoRun.pathInfo
/usr/share/augustus/scripts/bedgraph2wig.pl
/usr/share/augustus/scripts/blat2gbrowse.pl
/usr/share/augustus/scripts/blat2hints.pl
/usr/share/augustus/scripts/block2prfl.pl
/usr/share/augustus/scripts/cegma2gff.pl
/usr/share/augustus/scripts/checkParamArchive.pl
/usr/share/augustus/scripts/checkUTR
/usr/share/augustus/scripts/cleanDOSfasta.pl
/usr/share/augustus/scripts/clusterAndSplitGenes.pl
/usr/share/augustus/scripts/computeFlankingRegion.pl
/usr/share/augustus/scripts/createAugustusJoblist.pl
/usr/share/augustus/scripts/del_from_prfl.pl
/usr/share/augustus/scripts/evalCGP.pl
/usr/share/augustus/scripts/eval_dualdecomp.pl
/usr/share/augustus/scripts/eval_multi_gtf.pl
/usr/share/augustus/scripts/exonerate2hints.pl
/usr/share/augustus/scripts/exoniphyDb2hints.pl
/usr/share/augustus/scripts/extractTranscriptEnds.pl
/usr/share/augustus/scripts/filter-ppx.pl
/usr/share/augustus/scripts/filterGenes.pl
/usr/share/augustus/scripts/filterGenesIn.pl
/usr/share/augustus/scripts/filterGenesIn_mRNAname.pl
/usr/share/augustus/scripts/filterGenesOut_mRNAname.pl
/usr/share/augustus/scripts/filterInFrameStopCodons.pl
/usr/share/augustus/scripts/filterMaf.pl
/usr/share/augustus/scripts/filterPSL.pl
/usr/share/augustus/scripts/filterShrimp.pl
/usr/share/augustus/scripts/filterSpliceHints.pl
/usr/share/augustus/scripts/findGffNamesInFasta.pl
/usr/share/augustus/scripts/gbSmallDNA2gff.pl
/usr/share/augustus/scripts/gbrowse.conf
/usr/share/augustus/scripts/gbrowseold2gff3.pl
/usr/share/augustus/scripts/getAnnoFasta.pl
/usr/share/augustus/scripts/getAnnoFastaFromJoingenes.py
/usr/share/augustus/scripts/getLinesMatching.pl
/usr/share/augustus/scripts/gff2gbSmallDNA.pl
/usr/share/augustus/scripts/gff2ps_mycustom
/usr/share/augustus/scripts/gffGetmRNA.pl
/usr/share/augustus/scripts/gp2othergp.pl
/usr/share/augustus/scripts/gtf2aa.pl
/usr/share/augustus/scripts/gtf2bed.pl
/usr/share/augustus/scripts/gtf2gff.pl
/usr/share/augustus/scripts/gth2gtf.pl
/usr/share/augustus/scripts/hal2maf_split.pl
/usr/share/augustus/scripts/helpMod.pm
/usr/share/augustus/scripts/intron2exex.pl
/usr/share/augustus/scripts/joinPeptides.pl
/usr/share/augustus/scripts/join_aug_pred.pl
/usr/share/augustus/scripts/join_mult_hints.pl
/usr/share/augustus/scripts/maf2conswig.pl
/usr/share/augustus/scripts/makeMatchLists.pl
/usr/share/augustus/scripts/makeUtrTrainingSet.pl
/usr/share/augustus/scripts/maskNregions.pl
/usr/share/augustus/scripts/moveParameters.pl
/usr/share/augustus/scripts/msa2prfl.pl
/usr/share/augustus/scripts/new_species.pl
/usr/share/augustus/scripts/opt_init_and_term_probs.pl
/usr/share/augustus/scripts/optimize_augustus.pl
/usr/share/augustus/scripts/parseSim4Output.pl
/usr/share/augustus/scripts/partition_gtf2gb.pl
/usr/share/augustus/scripts/pasapolyA2hints.pl
/usr/share/augustus/scripts/peptides2alternatives.pl
/usr/share/augustus/scripts/peptides2hints.pl
/usr/share/augustus/scripts/phastconsDB2hints.pl
/usr/share/augustus/scripts/polyA2hints.pl
/usr/share/augustus/scripts/prints2prfl.pl
/usr/share/augustus/scripts/pslMap.pl
/usr/share/augustus/scripts/randomSplit.pl
/usr/share/augustus/scripts/ratewig.pl
/usr/share/augustus/scripts/retroDB2hints.pl
/usr/share/augustus/scripts/rmRedundantHints.pl
/usr/share/augustus/scripts/runAllSim4.pl
/usr/share/augustus/scripts/samMap.pl
/usr/share/augustus/scripts/scipiogff2gff.pl
/usr/share/augustus/scripts/setStopCodonFreqs.pl
/usr/share/augustus/scripts/simpleFastaHeaders.pl
/usr/share/augustus/scripts/simplifyFastaHeaders.pl
/usr/share/augustus/scripts/splitMfasta.pl
/usr/share/augustus/scripts/split_wiggle.pl
/usr/share/augustus/scripts/summarizeACGTcontent.pl
/usr/share/augustus/scripts/transMap2hints.pl
/usr/share/augustus/scripts/uniquePeptides.pl
/usr/share/augustus/scripts/utrgff2gbrowse.pl
/usr/share/augustus/scripts/webserver-results.body
/usr/share/augustus/scripts/webserver-results.head
/usr/share/augustus/scripts/webserver-results.tail
/usr/share/augustus/scripts/weedMaf.pl
/usr/share/augustus/scripts/wig2hints.pl
/usr/share/augustus/scripts/wigchoose.pl
/usr/share/augustus/scripts/writeResultsPage.pl
/usr/share/augustus/scripts/yaml2gff.1.4.pl
/usr/share/doc/augustus/HISTORY.TXT.gz
/usr/share/doc/augustus/changelog.Debian.gz
/usr/share/doc/augustus/changelog.gz
/usr/share/doc/augustus/copyright
/usr/share/man/man1/aln2wig.1.gz
/usr/share/man/man1/augustus.1.gz
/usr/share/man/man1/bam2hints.1.gz
/usr/share/man/man1/bam2wig.1.gz
/usr/share/man/man1/checkTargetSortedness.1.gz
/usr/share/man/man1/compileSpliceCands.1.gz
/usr/share/man/man1/etraining.1.gz
/usr/share/man/man1/fastBlockSearch.1.gz
/usr/share/man/man1/filterBam.1.gz
/usr/share/man/man1/homGeneMapping.1.gz
/usr/share/man/man1/joingenes.1.gz
/usr/share/man/man1/prepareAlign.1.gz
/usr/share/man/man1/utrrnaseq.1.gz