"Fossies" - the Fresh Open Source Software Archive

Contents of augustus-3.2.2.tar.gz (30 Mar 17:24, 116066704 Bytes)

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



Fossies path:  /linux/misc/augustus-3.2.2.tar.gz   [Download | Doxygen docs | Diffs report | CLOC analysis]
Alternative downloads:  tar.bz2 | tar.xz | zip
Member paths+URLs:  Full
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drwxrwxr-x        0 2016-03-30 17:12 
drwxr-xr-x        0 2015-09-25 12:18 examples/
drwxr-xr-x        0 2015-04-24 14:23 examples/autoAug/
-rw-r--r--  1682388 2015-04-24 14:23 examples/autoAug/cdna.fa
-rw-r--r--   447544 2015-04-24 14:23 examples/autoAug/traingenes.gb
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-rw-r--r--     1894 2015-04-24 14:23 examples/autoAug/README.TXT
-rw-r--r--    58784 2015-04-24 14:23 examples/autoAug/traingenes.gff
-rw-r--r--   339191 2015-04-24 14:23 examples/autoAug/cdna.psl
-rw-r--r--  1016673 2015-04-24 14:23 examples/autoAug/genome.fa
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drwxr-xr-x        0 2015-04-24 14:23 examples/profile/
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-rw-r--r--       76 2015-04-24 14:23 examples/hints.overlapexample.gff
-rw-r--r--     9620 2015-04-24 14:23 examples/HS04636.fa
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-rw-r--r--     2393 2015-04-24 14:23 examples/HS08198.fa
drwxr-xr-x        0 2015-10-14 10:06 examples/cgp/
-rw-r--r--    32647 2015-04-24 14:23 examples/cgp/human.fa
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-rw-r--r--     2776 2015-04-24 14:23 examples/cgp/cgp.extrinsic.cfg
-rw-r--r--    26428 2015-04-24 14:23 examples/cgp/mouse.fa
-rw-rw-r--      141 2015-09-21 09:44 examples/cgp/README.TXT
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-rw-r--r--       85 2015-04-24 14:23 examples/cgp/tree.nwk
-rw-rw-r--      224 2015-10-14 10:06 examples/cgp/genomes.tbl
-rw-r--r--   108967 2015-04-24 14:23 examples/cgp/aln.maf
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-rw-r--r--      571 2015-04-24 14:23 examples/overlapexample.fa
drwxr-xr-x        0 2016-03-30 17:10 scripts/
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-rwxr-xr-x     1716 2015-04-24 14:23 scripts/filterGenesOut_mRNAname.pl
-rwxr-xr-x      584 2015-04-24 14:23 scripts/ratewig.pl
-rwxr-xr-x     3022 2015-04-24 14:23 scripts/augustus2browser.pl
-rwxr-xr-x     4992 2015-04-24 14:23 scripts/samMap.pl
-rwxr-xr-x      531 2015-04-24 14:23 scripts/selectLongestORFs.pl
-rwxrwxr-x     2188 2016-03-14 17:26 scripts/filterGenesIn_mRNAname.pl
-rwxr-xr-x     1786 2015-04-24 14:23 scripts/splitMfasta.pl
-rwxr-xr-x     2395 2015-04-24 14:23 scripts/utrgff2gbrowse.pl
-rwxr-xr-x    16996 2015-04-24 14:23 scripts/gff2gbSmallDNA.pl
-rwxr-xr-x     2330 2015-04-24 14:23 scripts/polyA2hints.pl
-rwxrwxr-x    65114 2016-03-30 16:03 scripts/optimize_augustus.pl
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-rwxr-xr-x     4879 2015-04-24 14:23 scripts/createAugustusJoblist.pl
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-rwxrwxr-x     9675 2016-03-30 16:03 scripts/evalCGP.pl
-rwxr-xr-x      468 2015-04-24 14:23 scripts/makeMatchLists.pl
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-rwxr-xr-x      435 2015-04-24 14:23 scripts/filter-ppx.pl
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-rwxr-xr-x      723 2015-04-24 14:23 scripts/runAllSim4.pl
-rwxr-xr-x     1301 2015-04-24 14:23 scripts/exoniphyDb2hints.pl
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-rwxr-xr-x      507 2015-04-24 14:23 scripts/extractTranscriptEnds.pl
-rwxr-xr-x    12539 2015-04-24 14:23 scripts/README.autoAug
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-rwxr-xr-x     8749 2015-04-24 14:23 scripts/join_aug_pred.pl
-rwxr-xr-x     1964 2015-04-24 14:23 scripts/uniquePeptides.pl
-rwxr-xr-x     2015 2015-04-24 14:23 scripts/moveParameters.pl
-rwxrwxr-x    12589 2015-07-16 12:38 scripts/hal2maf_split.pl
-rwxr-xr-x      850 2015-04-24 14:23 scripts/filterGenes.pl
-rwxr-xr-x    13647 2015-04-24 14:23 scripts/gtf2gff.pl
-rwxr-xr-x     8166 2015-04-24 14:23 scripts/helpMod.pm
-rwxr-xr-x     3043 2015-04-24 14:23 scripts/exonerate2hints.pl
-rwxr-xr-x    44143 2015-04-24 14:23 scripts/autoAugTrain.pl
-rwxr-xr-x     3369 2015-04-24 14:23 scripts/peptides2alternatives.pl
-rwxr-xr-x    48984 2015-04-24 14:23 scripts/autoAug.pl
-rwxr-xr-x     2598 2016-03-30 16:05 scripts/simplifyFastaHeaders.pl
-rwxr-xr-x     3769 2015-04-24 14:23 scripts/gbrowseold2gff3.pl
-rwxr-xr-x    10571 2015-04-24 14:23 scripts/prints2prfl.pl
-rwxrwxr-x    18606 2015-07-16 12:38 scripts/transMap2hints.pl
-rwxr-xr-x     3105 2015-04-24 14:23 scripts/webserver-results.tail
-rwxr-xr-x     7113 2015-04-24 14:23 scripts/new_species.pl
-rwxr-xr-x     3606 2015-04-24 14:23 scripts/parseSim4Output.pl
-rwxr-xr-x     2158 2015-04-24 14:23 scripts/summarizeACGTcontent.pl
-rwxr-xr-x     2081 2015-04-24 14:23 scripts/filterSpliceHints.pl
-rwxrwxr-x     1230 2015-07-16 12:38 scripts/join_mult_hints.pl
-rwxr-xr-x     1946 2015-04-24 14:23 scripts/retroDB2hints.pl
-rwxr-xr-x     7558 2015-04-24 14:23 scripts/clusterAndSplitGenes.pl
-rwxr-xr-x     4442 2015-04-24 14:23 scripts/blat2gbrowse.pl
-rwxr-xr-x    15629 2015-04-24 14:23 scripts/writeResultsPage.pl
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-rwxr-xr-x     8032 2015-04-24 14:23 scripts/pslMap.pl
-rwxrwxr-x     2233 2015-07-16 12:38 scripts/cegma2gff.pl
-rw-rw-r--      681 2016-03-30 16:40 common.mk
-rw-r--r--    28114 2015-09-25 12:29 retraining.html
drwxr-xr-x        0 2016-03-30 17:39 bin/
-rwxrwxr-x   524704 2016-03-30 17:09 bin/filterBam
-rwxrwxr-x  1835944 2016-03-30 17:08 bin/etraining
-rwxrwxr-x    43336 2016-03-30 17:07 bin/prepareAlign
-rwxrwxr-x   371480 2016-03-30 17:08 bin/fastBlockSearch
-rwxrwxr-x  1634408 2016-03-30 17:08 bin/augustus
-rwxrwxr-x    42168 2016-03-30 17:09 bin/bam2hints
-rwxrwxr-x   435880 2016-03-30 17:11 bin/joingenes
-rwxrwxr-x   150720 2016-03-30 17:10 bin/homGeneMapping
-rw-rw-r--    20859 2016-03-14 17:26 README-cgp.txt
-rw-rw-r--    53244 2016-03-30 16:22 README.TXT
drwxr-xr-x        0 2015-07-16 12:38 config/
drwxr-xr-x        0 2015-04-24 14:24 config/profile/
-rwxr-xr-x     1752 2015-04-24 14:24 config/profile/blosum62.qij
-rwxr-xr-x     1752 2015-04-24 14:24 config/profile/blosum55.qij
lrwxrwxrwx        0 2015-04-24 14:24 config/profile/default.qij -> blosum62.qij
drwxr-xr-x        0 2016-03-14 17:26 config/extrinsic/
-rw-r--r--     2552 2015-04-24 14:24 config/extrinsic/extrinsic.M.RM.E.W.cfg
-rw-r--r--     2441 2016-03-14 17:26 config/extrinsic/extrinsic.M.RM.PB.cfg
-rw-r--r--     2033 2015-04-24 14:24 config/extrinsic/extrinsic.E.cfg
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-rw-r--r--     3108 2015-04-24 14:24 config/extrinsic/cgp.extrinsic.cfg
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-rw-r--r--     2608 2015-04-24 14:24 config/extrinsic/extrinsic.MPE.cfg
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drwxr-xr-x        0 2015-04-28 15:31 config/model/
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-rw-r--r--     3086 2015-04-24 14:24 config/model/states_singlestrand_2igenic.cfg
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drwxrwxr-x        0 2016-03-14 17:26 config/cgp/
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drwxr-xr-x        0 2016-03-30 17:38 config/species/
drwxr-xr-x        0 2015-04-24 14:23 config/species/parasteatoda/
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drwxr-xr-x        0 2015-04-24 14:23 config/species/zebrafish/
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drwxr-xr-x        0 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/
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   MD5 (augustus-3.2.2.tar.gz): 248dc183ef10b6b5ba8256d7599f9a47
  SHA1 (augustus-3.2.2.tar.gz): c4c7651655273a957ebe7714570c1ccda61a9c07
SHA256 (augustus-3.2.2.tar.gz): 909f0e87ec9a44bcd22fdf69e0c12ea2f060194a1bf85ce10ed626745a204f62

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