"Fossies" - the Fresh Open Source Software Archive  

Source code changes report for "augustus" between the packages
augustus-3.3.2.tar.gz and augustus-3.3.3.tar.gz

About: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

Summary:

The "augustus" source code changed by about 36.3% and now consists of 1995 regular files (+147), 9 symbolic links (+8) and 254 directories (+15).

Related Informations:

See HISTORY.TXT (augustus 3.3.3).

Changes In Files (According File Type):

File TypeTotalAddedRemovedChanged
Header file 99 23 0 57
C program 9 2 0 1
C++ program 106 12 0 76
Perl module 3 0 0 0
Perl program 100 3 1 93
Python program 3 2 0 1
Shell program 5 0 0 0
Configuration file 297 2 0 109
Executable file 15 7 3 2
JavaScript file 3 0 0 0
JSON file 128 0 1 0
Makefile 22 2 1 6
Man page 12 0 0 2
Symbolic link 9 8 0 0
Berkeley database 3 2 0 0
Compiled object 2 0 1 1
CSS style sheet 4 0 0 0
Data List 5 0 0 0
Doxygen file 1 0 0 0
Git file 2 2 0 0
HTML page 43 0 2 11
MS office document 3 0 0 0
Options file 1 0 0 1
TeX document 1 0 0 0
YAML file 1 0 1 0
Audio file 2 0 0 0
Data file 92 11 0 0
Image file 5 0 0 0
PDF file 9 0 0 0
Vector Image file 1 0 0 0
Directory 257 18 3 0
Archive 13 0 0 0
Information file 2 0 0 1
License 5 2 1 1
Readme file 43 2 3 7
Text file 966 107 18 95
Other 21 0 0 0
Total Files229320535464



Header Files (80 of 99):

NameStatusDeltaVisual Diff
auxprogs/filterBam/src/headers/filterBam.h changed 0.7% diff
auxprogs/homGeneMapping/include/bitmasking.hh changed 1.6% diff
auxprogs/homGeneMapping/include/gene.hh changed 0.9% diff
auxprogs/homGeneMapping/include/genome.hh changed 0.7% diff
auxprogs/homGeneMapping/include/projectio.hh changed 2.5% diff
auxprogs/homGeneMapping/include/sqliteDB.hh changed 2.1% diff
include/alignment.hh changed 7.9% diff
include/baumwelch.hh changed 19.0% diff
include/codonMSA.hh changed 55.0% diff
include/commontrain.hh changed 26.3% diff
include/compgenepred.hh changed 55.0% diff
include/consensus.hh changed 20.5% diff
include/contentmodel.hh changed 27.1% diff
include/contTimeMC.hh changed 10.3% diff
include/evaluation.hh changed 10.7% diff
include/exon_seg.hh changed 11.7% diff
include/exoncand.hh changed 22.9% diff
include/exonmodel.hh changed 14.4% diff
include/extrinsicinfo.hh changed 9.4% diff
include/fasta.hh changed 41.7% diff
include/genbank.hh changed 27.1% diff
include/gene.hh changed 5.5% diff
include/geneMSA.hh changed 5.4% diff
include/geneticcode.hh changed 6.9% diff
include/genomicMSA.hh changed 10.4% diff
include/graph.hh changed 7.7% diff
include/hints.hh changed 10.2% diff
include/igenicmodel.hh changed 21.4% diff
include/intronmodel.hh changed 10.9% diff
include/liftover.hh changed 12.1% diff
include/lldouble.hh changed 13.7% diff
include/matrix.hh changed 30.6% diff
include/mea.hh changed 14.3% diff
include/meaPath.hh changed 38.8% diff
include/merkmal.hh changed 10.5% diff
include/motif.hh changed 22.0% diff
include/namgene.hh changed 7.4% diff
include/ncmodel.hh changed 17.4% diff
include/orthoexon.hh changed 7.1% diff
include/orthogene.hh changed 76.0% diff
include/orthograph.hh changed 6.7% diff
include/phylotree.hh changed 8.4% diff
include/pp_fastBlockSearcher.hh changed 3.2% diff
include/pp_hitseq.hh changed 4.0% diff
include/pp_profile.hh changed 3.1% diff
include/pp_scoring.hh changed 3.6% diff
include/projectio.hh changed 21.1% diff
include/properties.hh changed 16.5% diff
include/randseqaccess.hh changed 17.0% diff
include/speciesgraph.hh changed 8.0% diff
include/sqliteDB.hh changed 21.5% diff
include/statemodel.hh changed 13.8% diff
include/table_structure.h changed 8.4% diff
include/train_logReg_param.hh changed 24.0% diff
include/types.hh changed 4.0% diff
include/utrmodel.hh changed 6.2% diff
include/vitmatrix.hh changed 6.4% diff
src/googletest/include/gtest/gtest-death-test.h added
src/googletest/include/gtest/gtest-matchers.h added
src/googletest/include/gtest/gtest-message.h added
src/googletest/include/gtest/gtest-param-test.h added
src/googletest/include/gtest/gtest-printers.h added
src/googletest/include/gtest/gtest-spi.h added
src/googletest/include/gtest/gtest-test-part.h added
src/googletest/include/gtest/gtest-typed-test.h added
src/googletest/include/gtest/gtest.h added
src/googletest/include/gtest/gtest_pred_impl.h added
src/googletest/include/gtest/gtest_prod.h added
src/googletest/include/gtest/internal/custom/gtest-port.h added
src/googletest/include/gtest/internal/custom/gtest-printers.h added
src/googletest/include/gtest/internal/custom/gtest.h added
src/googletest/include/gtest/internal/gtest-death-test-internal.h added
src/googletest/include/gtest/internal/gtest-filepath.h added
src/googletest/include/gtest/internal/gtest-internal.h added
src/googletest/include/gtest/internal/gtest-param-util.h added
src/googletest/include/gtest/internal/gtest-port-arch.h added
src/googletest/include/gtest/internal/gtest-port.h added
src/googletest/include/gtest/internal/gtest-string.h added
src/googletest/include/gtest/internal/gtest-type-util.h added
src/googletest/src/gtest-internal-inl.h added

C Programs (3 of 9):

NameStatusDeltaVisual Diff
auxprogs/bam2wig/bam2wig.c changed 3.6% diff
docs/CHANGE-TREE-PARSER.md added
src/googletest/include/gtest/internal/gtest-type-util.h.pump added

C++ Programs (88 of 106):

NameStatusDeltaVisual Diff
auxprogs/bam2hints/bam2hints.cc changed 2.0% diff
auxprogs/filterBam/src/filterBam.cc changed 0.05% diff
auxprogs/filterBam/src/functions/initOptions.cc changed 0.3% diff
auxprogs/filterBam/src/functions/MatePairs.cc changed 1.9% diff
auxprogs/filterBam/src/functions/PairednessCoverage.cc changed 2.0% diff
auxprogs/filterBam/src/functions/SingleAlignment.cc changed 0.7% diff
auxprogs/homGeneMapping/src/gene.cc changed 0.8% diff
auxprogs/homGeneMapping/src/genome.cc changed 0.2% diff
auxprogs/homGeneMapping/src/main.cc changed 0.4% diff
auxprogs/homGeneMapping/src/sqliteDB.cc changed 2.1% diff
src/alignment.cc changed 1.8% diff
src/augustus.cc changed 2.4% diff
src/baumwelch.cc changed 4.0% diff
src/codonMSA.cc changed 11.2% diff
src/commontrain.cc changed 8.4% diff
src/compgenepred.cc changed 5.9% diff
src/consensus.cc changed 6.0% diff
src/consensusFinder.cc changed 4.7% diff
src/contentmodel.cc changed 6.7% diff
src/contTimeMC.cc changed 2.0% diff
src/curve2hints.cc changed 5.0% diff
src/dummy.cc changed 31.0% diff
src/espoca.cc changed 16.9% diff
src/etraining.cc changed 3.7% diff
src/evaluate.cc changed 27.8% diff
src/evaluation.cc changed 2.2% diff
src/exon_seg.cc changed 4.6% diff
src/exoncand.cc changed 3.2% diff
src/exonmodel.cc changed 3.9% diff
src/exontrain.cc changed 2.0% diff
src/extrinsicinfo.cc changed 2.5% diff
src/fasta.cc changed 10.1% diff
src/fastBlockSearch.cc changed 2.2% diff
src/genbank.cc changed 4.3% diff
src/gene.cc changed 1.1% diff
src/geneMSA.cc changed 1.0% diff
src/geneticcode.cc changed 5.0% diff
src/genomicMSA.cc changed 1.9% diff
src/getSeq.cc changed 16.0% diff
src/googletest/src/gtest-all.cc added
src/googletest/src/gtest-death-test.cc added
src/googletest/src/gtest-filepath.cc added
src/googletest/src/gtest-matchers.cc added
src/googletest/src/gtest-port.cc added
src/googletest/src/gtest-printers.cc added
src/googletest/src/gtest-test-part.cc added
src/googletest/src/gtest-typed-test.cc added
src/googletest/src/gtest.cc added
src/googletest/src/gtest_main.cc added
src/graph.cc changed 0.4% diff
src/hints.cc changed 3.4% diff
src/igenicmodel.cc changed 7.0% diff
src/igenictrain.cc changed 5.9% diff
src/intronmodel.cc changed 5.0% diff
src/introntrain.cc changed 2.8% diff
src/lldouble.cc changed 7.8% diff
src/load2db.cc changed 3.7% diff
src/load2sqlitedb.cc changed 5.6% diff
src/logdoubletest.cc changed 17.8% diff
src/mea.cc changed 1.0% diff
src/meaPath.cc changed 5.1% diff
src/merkmal.cc changed 1.9% diff
src/motif.cc changed 5.2% diff
src/namgene.cc changed 3.1% diff
src/ncmodel.cc changed 2.9% diff
src/orthoexon.cc changed 4.1% diff
src/orthogene.cc changed 97.1% diff
src/orthograph.cc changed 2.0% diff
src/phylotree.cc changed 3.6% diff
src/pp_fastBlockSearcher.cc changed 7.7% diff
src/pp_hitseq.cc changed 28.1% diff
src/pp_prepare_align.cc changed 1.2% diff
src/pp_profile.cc changed 4.2% diff
src/pp_scoring.cc changed 2.0% diff
src/projectio.cc changed 70.0% diff
src/properties.cc changed 3.9% diff
src/randseqaccess.cc changed 2.7% diff
src/scanner/lex.cc changed 0.2% diff
src/speciesgraph.cc changed 2.4% diff
src/sqliteDB.cc changed 8.0% diff
src/statemodel.cc changed 6.3% diff
src/train_logReg_param.cc changed 2.6% diff
src/types.cc changed 7.1% diff
src/unittests/fasta_unittest.cc added
src/unittests/lldouble_unittest.cc added
src/utrmodel.cc changed 4.0% diff
src/utrtrain.cc changed 3.2% diff
src/vitmatrix.cc changed 2.5% diff

Perl Programs (97 of 100):

NameStatusDeltaVisual Diff
docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl changed 0.7% diff
docs/tutorial2018/BRAKER_v2.0.4+/braker.pl changed 0.2% diff
docs/tutorial2018/BRAKER_v2.0.4+/filterGenemark.pl changed 0.5% diff
docs/tutorial2018/BRAKER_v2.0.4+/filterIntronsFindStrand.pl changed 1.8% diff
docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl changed 0.3% diff
scripts/aa2nonred.pl changed 51.5% diff
scripts/augustus2browser.pl changed 0.7% diff
scripts/augustus2gbrowse.pl changed 5.7% diff
scripts/autoAug.pl changed 18.3% diff
scripts/autoAugPred.pl changed 3.0% diff
scripts/autoAugTrain.pl changed 1.2% diff
scripts/bedgraph2wig.pl changed 0.7% diff
scripts/blat2gbrowse.pl changed 0.5% diff
scripts/blat2hints.pl changed 0.6% diff
scripts/block2prfl.pl changed 0.2% diff
scripts/cegma2gff.pl changed 1.0% diff
scripts/checkParamArchive.pl changed 0.6% diff
scripts/cleanDOSfasta.pl changed 4.1% diff
scripts/clusterAndSplitGenes.pl changed 0.3% diff
scripts/compare_masking.pl added
scripts/computeFlankingRegion.pl changed 1.0% diff
scripts/createAugustusJoblist.pl changed 0.3% diff
scripts/del_from_prfl.pl changed 0.8% diff
scripts/eval_dualdecomp.pl changed 0.2% diff
scripts/eval_multi_gtf.pl changed 0.6% diff
scripts/evalCGP.pl changed 0.2% diff
scripts/exonerate2hints.pl changed 0.7% diff
scripts/exoniphyDb2hints.pl changed 1.7% diff
scripts/extractTranscriptEnds.pl changed 4.3% diff
scripts/filter-ppx.pl changed 5.7% diff
scripts/filterGenes.pl changed 2.6% diff
scripts/filterGenesIn.pl changed 2.1% diff
scripts/filterGenesIn_mRNAname.pl changed 0.8% diff
scripts/filterGenesOut_mRNAname.pl changed 1.3% diff
scripts/filterInFrameStopCodons.pl changed 2.0% diff
scripts/filterMaf.pl changed 0.8% diff
scripts/filterPSL.pl changed 0.1% diff
scripts/filterShrimp.pl changed 0.5% diff
scripts/filterSpliceHints.pl changed 1.1% diff
scripts/findGffNamesInFasta.pl changed 1.3% diff
scripts/fix_joingenes_gtf.pl added
scripts/gbrowseold2gff3.pl changed 0.6% diff
scripts/gbSmallDNA2gff.pl changed 0.7% diff
scripts/getAnnoFasta.pl changed 0.3% diff
scripts/getLinesMatching.pl changed 1.1% diff
scripts/gff2gbSmallDNA.pl changed 0.2% diff
scripts/gffGetmRNA.pl changed 0.5% diff
scripts/gp2othergp.pl changed 0.7% diff
scripts/gtf2aa.pl changed 0.3% diff
scripts/gtf2bed.pl changed 0.2% diff
scripts/gtf2gff.pl changed 17.8% diff
scripts/gth2gtf.pl changed 0.8% diff
scripts/hal2maf_split.pl changed 0.2% diff
scripts/intron2exex.pl removed
scripts/join_aug_pred.pl changed 0.2% diff
scripts/join_mult_hints.pl changed 0.8% diff
scripts/joinPeptides.pl changed 1.5% diff
scripts/maf2conswig.pl changed 0.6% diff
scripts/makeMatchLists.pl changed 4.7% diff
scripts/makeUtrTrainingSet.pl changed 0.1% diff
scripts/maskNregions.pl changed 1.3% diff
scripts/merge_masking.pl added
scripts/moveParameters.pl changed 1.1% diff
scripts/msa2prfl.pl changed 0.1% diff
scripts/new_species.pl changed 0.3% diff
scripts/opt_init_and_term_probs.pl changed 0.3% diff
scripts/optimize_augustus.pl changed 0.03% diff
scripts/parseSim4Output.pl changed 0.6% diff
scripts/partition_gtf2gb.pl changed 0.1% diff
scripts/pasapolyA2hints.pl changed 1.0% diff
scripts/peptides2alternatives.pl changed 0.7% diff
scripts/peptides2hints.pl changed 0.3% diff
scripts/phastconsDB2hints.pl changed 0.8% diff
scripts/polyA2hints.pl changed 0.9% diff
scripts/prints2prfl.pl changed 0.2% diff
scripts/pslMap.pl changed 0.3% diff
scripts/randomSplit.pl changed 1.1% diff
scripts/ratewig.pl changed 3.8% diff
scripts/retroDB2hints.pl changed 1.1% diff
scripts/rmRedundantHints.pl changed 1.6% diff
scripts/runAllSim4.pl changed 3.0% diff
scripts/samMap.pl changed 0.4% diff
scripts/scipiogff2gff.pl changed 1.9% diff
scripts/setStopCodonFreqs.pl changed 1.0% diff
scripts/simpleFastaHeaders.pl changed 1.8% diff
scripts/simplifyFastaHeaders.pl changed 0.8% diff
scripts/split_wiggle.pl changed 2.6% diff
scripts/splitMfasta.pl changed 1.0% diff
scripts/summarizeACGTcontent.pl changed 1.0% diff
scripts/transMap2hints.pl changed 0.1% diff
scripts/uniquePeptides.pl changed 4.0% diff
scripts/utrgff2gbrowse.pl changed 0.9% diff
scripts/weedMaf.pl changed 1.4% diff
scripts/wig2hints.pl changed 0.4% diff
scripts/wigchoose.pl changed 0.8% diff
scripts/writeResultsPage.pl changed 33.9% diff
scripts/yaml2gff.1.4.pl changed 0.3% diff

Python Programs (all 3):

NameStatusDeltaVisual Diff
scripts/bamToWig.py added
scripts/fix_in_frame_stop_codon_genes.py added
scripts/getAnnoFastaFromJoingenes.py changed 81.2% diff

Configuration Files (111 of 297):

NameStatusDeltaVisual Diff
config/species/adorsata/adorsata_parameters.cfg changed 3.2% diff
config/species/aedes/aedes_parameters.cfg changed 1.6% diff
config/species/amphimedon/amphimedon_parameters.cfg changed 2.5% diff
config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg changed 3.8% diff
config/species/anidulans/anidulans_parameters.cfg changed 1.6% diff
config/species/arabidopsis/arabidopsis_parameters.cfg changed 2.2% diff
config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg changed 2.7% diff
config/species/aspergillus_nidulans/aspergillus_nidulans_parameters.cfg changed 2.7% diff
config/species/aspergillus_oryzae/aspergillus_oryzae_parameters.cfg changed 2.7% diff
config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg changed 2.7% diff
config/species/b_pseudomallei/b_pseudomallei_parameters.cfg changed 3.6% diff
config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg changed 3.8% diff
config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg changed 3.8% diff
config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg changed 2.7% diff
config/species/brugia/brugia_parameters.cfg changed 1.6% diff
config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg changed 3.8% diff
config/species/cacao/cacao_parameters.cfg changed 3.6% diff
config/species/caenorhabditis/caenorhabditis_parameters.cfg changed 4.2% diff
config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg changed 3.8% diff
config/species/candida_albicans/candida_albicans_parameters.cfg changed 2.7% diff
config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg changed 2.7% diff
config/species/candida_tropicalis/candida_tropicalis_parameters.cfg changed 2.7% diff
config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg changed 2.7% diff
config/species/chicken/chicken_parameters.cfg changed 3.7% diff
config/species/chiloscyllium/chiloscyllium_parameters.cfg changed 3.7% diff
config/species/chlamy2011/chlamy2011_parameters.cfg changed 2.4% diff
config/species/chlamydomonas/chlamydomonas_parameters.cfg changed 2.5% diff
config/species/chlorella/chlorella_parameters.cfg changed 2.5% diff
config/species/ciona/ciona_parameters.cfg changed 3.7% diff
config/species/coccidioides_immitis/coccidioides_immitis_parameters.cfg changed 2.7% diff
config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg changed 3.8% diff
config/species/coprinus/coprinus_parameters.cfg changed 1.6% diff
config/species/coprinus_cinereus/coprinus_cinereus_parameters.cfg changed 2.7% diff
config/species/coyote_tobacco/coyote_tobacco_parameters.cfg changed 3.7% diff
config/species/cryptococcus/cryptococcus_parameters.cfg changed 1.5% diff
config/species/cryptococcus_neoformans_gattii/cryptococcus_neoformans_gattii_parameters.cfg changed 2.8% diff
config/species/cryptococcus_neoformans_neoformans_B/cryptococcus_neoformans_neoformans_B_parameters
.cfg
changed 2.9% diff
config/species/cryptococcus_neoformans_neoformans_JEC21/cryptococcus_neoformans_neoformans_JEC21_pa
rameters.cfg
changed 2.9% diff
config/species/culex/culex_parameters.cfg changed 2.6% diff
config/species/culex/culex_parameters.old.cfg changed 2.6% diff
config/species/debaryomyces_hansenii/debaryomyces_hansenii_parameters.cfg changed 2.7% diff
config/species/E_coli_K12/E_coli_K12_parameters.cfg changed 3.6% diff
config/species/elephant_shark/elephant_shark_parameters.cfg changed 3.7% diff
config/species/encephalitozoon_cuniculi_GB/encephalitozoon_cuniculi_GB_parameters.cfg changed 2.8% diff
config/species/eremothecium_gossypii/eremothecium_gossypii_parameters.cfg changed 2.7% diff
config/species/fly/fly_parameters.cfg changed 3.7% diff
config/species/fly_exp/fly_exp_parameters.cfg changed 3.7% diff
config/species/fusarium/fusarium_parameters.cfg changed 1.6% diff
config/species/fusarium_graminearum/fusarium_graminearum_parameters.cfg changed 2.7% diff
config/species/galdieria/galdieria_parameters.cfg changed 1.0% diff
config/species/generic/generic_parameters.cfg changed 3.7% diff
config/species/heliconius_melpomene1/heliconius_melpomene1_parameters.cfg changed 3.8% diff
config/species/histoplasma/histoplasma_parameters.cfg changed 1.6% diff
config/species/histoplasma_capsulatum/histoplasma_capsulatum_parameters.cfg changed 2.7% diff
config/species/honeybee1/honeybee1_parameters.cfg changed 3.7% diff
config/species/human/human_parameters.cfg changed 1.0% diff
config/species/japaneselamprey/japaneselamprey_parameters.cfg changed 3.8% diff
config/species/kluyveromyces_lactis/kluyveromyces_lactis_parameters.cfg changed 2.7% diff
config/species/laccaria_bicolor/laccaria_bicolor_parameters.cfg changed 2.7% diff
config/species/leishmania_tarentolae/leishmania_tarentolae_parameters.cfg changed 3.9% diff
config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg changed 2.7% diff
config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg changed 2.7% diff
config/species/maize/maize_parameters.cfg changed 5.2% diff
config/species/maize5/maize5_parameters.cfg changed 3.7% diff
config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg changed 3.8% diff
config/species/nasonia/nasonia_parameters.cfg changed 2.5% diff
config/species/nematostella_vectensis/nematostella_vectensis_parameters.cfg changed 3.8% diff
config/species/neurospora/neurospora_parameters.cfg changed 1.5% diff
config/species/neurospora_crassa/neurospora_crassa_parameters.cfg changed 2.7% diff
config/species/parasteatoda/parasteatoda_parameters.cfg changed 3.7% diff
config/species/pchrysosporium/pchrysosporium_parameters.cfg changed 1.5% diff
config/species/pea_aphid/pea_aphid_parameters.cfg changed 2.5% diff
config/species/pfalciparum/pfalciparum_parameters.cfg changed 4.9% diff
config/species/phanerochaete_chrysosporium/phanerochaete_chrysosporium_parameters.cfg changed 2.8% diff
config/species/pichia_stipitis/pichia_stipitis_parameters.cfg changed 2.6% diff
config/species/pisaster/pisaster_parameters.cfg changed 3.7% diff
config/species/pneumocystis/pneumocystis_parameters.cfg changed 2.6% diff
config/species/rhincodon/rhincodon_parameters.cfg changed 3.7% diff
config/species/rhizopus_oryzae/rhizopus_oryzae_parameters.cfg changed 2.6% diff
config/species/rhodnius/rhodnius_parameters.cfg changed 3.7% diff
config/species/rice/rice_parameters.cfg changed 3.7% diff
config/species/s_aureus/s_aureus_parameters.cfg changed 3.5% diff
config/species/s_pneumoniae/s_pneumoniae_parameters.cfg changed 3.6% diff
config/species/saccharomyces/saccharomyces_parameters.cfg changed 1.5% diff
config/species/saccharomyces_cerevisiae_rm11-1a_1/saccharomyces_cerevisiae_rm11-1a_1_parameters.cfg changed 2.8% diff
config/species/saccharomyces_cerevisiae_S288C/saccharomyces_cerevisiae_S288C_parameters.cfg changed 2.8% diff
config/species/schistosoma/schistosoma_parameters.cfg changed 3.6% diff
config/species/schistosoma2/schistosoma2_parameters.cfg changed 3.7% diff
config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg changed 2.7% diff
config/species/scyliorhinus/scyliorhinus_parameters.cfg changed 3.7% diff
config/species/sealamprey/sealamprey_parameters.cfg changed 2.5% diff
config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg changed 3.9% diff
config/species/sulfolobus_solfataricus/sulfolobus_solfataricus_parameters.cfg changed 3.7% diff
config/species/template_prokaryotic/template_prokaryotic_parameters.cfg changed 3.7% diff
config/species/tetrahymena/tetrahymena_parameters.cfg changed 3.5% diff
config/species/thermoanaerobacter_tengcongensis/thermoanaerobacter_tengcongensis_parameters.cfg changed 3.8% diff
config/species/tomato/tomato_parameters.cfg changed 3.7% diff
config/species/toxoplasma/toxoplasma_parameters.cfg changed 4.1% diff
config/species/tribolium2012/tribolium2012_parameters.cfg changed 2.5% diff
config/species/trichinella/trichinella_parameters.cfg changed 3.7% diff
config/species/ustilago/ustilago_parameters.cfg changed 1.5% diff
config/species/ustilago_maydis/ustilago_maydis_parameters.cfg changed 2.6% diff
config/species/verticillium_albo_atrum1/verticillium_albo_atrum1_parameters.cfg changed 3.8% diff
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docs/tutorial-cgp/results/aug_rnaseq/hg38.gff changed 0.3% diff
docs/tutorial-cgp/results/aug_rnaseq/mm10.gff changed 0.3% diff
docs/tutorial-cgp/results/aug_rnaseq/monDom5.gff changed 0.7% diff
docs/tutorial-cgp/results/aug_rnaseq/rheMac3.gff changed 0.4% diff
docs/tutorial-cgp/results/aug_rnaseq/rn6.gff changed 1.9% diff
docs/tutorial/results/augustus-ppx.gff changed 0.4% diff
docs/tutorial/results/augustus.abinitio.gff changed 0.02% diff
docs/tutorial/results/augustus.hints.gff changed 0.003% diff
docs/tutorial/results/genes.gb removed
docs/tutorial/results/genes.gb.train removed
docs/tutorial/results/output-abinitio.gff changed 1.0% diff
docs/tutorial/results/output.gff changed 0.4% diff
docs/tutorial2018/data/augustus_ab_initio.gff changed 0.01% diff
examples/cgp/human.hints.gff changed 0.1% diff
examples/cgp/out/bosTau4.cgp.gff removed
examples/cgp/out/galGal3.cgp.gff removed
examples/cgp/out/hg19.cgp.gff removed
examples/cgp/out/mm9.cgp.gff removed
examples/profile/chr1.161M.gff changed 0.4% diff
mansrc/bam2hints.1.adoc changed 9.2% diff
mansrc/homGeneMapping.1.adoc changed 3.2% diff
src/cxxflags added
src/unittests/test.fa added

Packages Compared:

augustus-3.3.2.tar.gz
augustus-3.3.3.tar.gz


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