"Fossies" - the Fresh Open Source Software Archive

Contents of augustus-3.4.0.tar.gz (11 Dec 17:43, 162498073 Bytes)

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



Fossies downloads: /linux/miscaugustus-3.4.0.tar.gz  (tar.bz2|tar.xz|zip)
Fossies services: Doxygen docs | Diffs report | CLOC analysis
Original URL: http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.4.0.tar.gz
Home page: https://bioinf.uni-greifswald.de/webaugustus/
VirusTotal check: Ok
Member paths+URLs:  Shortened | full
Member sort order:  docs related (infos|docs|other) | original | size (top100) | date | path | name | ext | top-path files

Basic infos (README, FAQ, INSTALL, ChangeLog, ...):
-rw-rw-r--     6096 2020-12-11 16:40 README.md
-rw-rw-r--      786 2019-05-22 10:34 docs/CDS.sp.README
-rw-rw-r--     2736 2019-05-22 10:34 docs/CHANGE-TREE-PARSER.md
-rw-rw-r--    22634 2020-12-11 16:01 docs/HISTORY.TXT
-rw-rw-r--     4968 2019-05-22 10:34 src/LICENSE.TXT
-rw-rw-r--    12674 2019-09-13 13:58 scripts/README.autoAug
-rw-rw-r--     2004 2020-12-11 16:40 docs/README-cgp.md
-rw-rw-r--     7791 2020-12-10 14:35 docs/README_ppsimscore.txt
-rw-rw-r--    18780 2019-05-22 10:34 docs/readme.rnaseq.html
-rw-rw-r--    54375 2020-12-09 14:14 docs/tutorial2018/README_augustus.TXT
-rw-rw-r--     1735 2020-12-09 14:14 auxprogs/bam2wig/README.md
-rw-rw-r--     1851 2019-05-22 10:34 auxprogs/utrrnaseq/README
-rw-rw-r--     1855 2019-05-22 10:34 auxprogs/bam2hints/README
-rw-rw-r--     2842 2019-05-22 10:34 docs/espoca/README
-rw-rw-r--     3355 2019-05-22 10:34 auxprogs/filterBam/README
-rw-rw-r--      545 2019-05-22 10:34 auxprogs/auxBamFilters/README
-rw-rw-r--      141 2019-05-22 10:34 examples/cgp/README.TXT
-rw-rw-r--     1894 2019-05-22 10:34 examples/autoAug/README.TXT
-rw-rw-r--     5134 2020-12-09 14:14 auxprogs/homGeneMapping/README.TXT

Basic docs (manual pages, PDF-,HTML-,/doc/-files, ...):
-rw-rw-r--     1500 2020-12-09 14:14 Dockerfile
-rw-rw-r--     5661 2020-12-11 16:32 docs/ABOUT.md
-rw-rw-r--      453 2020-12-09 14:14 mansrc/aln2wig.1.adoc
-rw-rw-r--      878 2020-12-09 14:14 mansrc/aln2wig.1
-rw-rw-r--     2874 2020-12-09 14:14 mansrc/augustus.1.adoc
-rw-rw-r--     3933 2020-12-09 14:14 mansrc/augustus.1
-rw-rw-r--     3224 2020-11-13 07:52 docs/AUGUSTUS-ON-WINDOWS.md
-rw-rw-r--     2552 2020-12-09 14:14 mansrc/bam2hints.1.adoc
-rw-rw-r--     3283 2020-12-09 14:14 mansrc/bam2hints.1
-rw-rw-r--      798 2020-12-09 14:14 mansrc/bam2wig.1.adoc
-rw-rw-r--     1225 2020-12-09 14:14 mansrc/bam2wig.1
-rw-rw-r--     8969 2019-05-22 10:34 docs/CDS.sp.pdf
-rw-rw-r--      970 2020-12-09 14:14 mansrc/compileSpliceCands.1.adoc
-rw-rw-r--     1469 2020-12-09 14:14 mansrc/compileSpliceCands.1
-rw-rw-r--      655 2020-09-11 10:44 docs/CONTACT.md
-rw-rw-r--      699 2020-12-09 14:14 mansrc/etraining.1.adoc
-rw-rw-r--     1111 2020-12-09 14:14 mansrc/etraining.1
-rw-rw-r--     4640 2020-09-15 10:33 docs/EXONCAND-MSAS-CGP.md
-rw-rw-r--     1925 2019-05-22 10:34 mansrc/fastBlockSearch.1.adoc
-rw-rw-r--     2446 2020-12-09 14:14 mansrc/fastBlockSearch.1
-rw-rw-r--     2815 2020-12-09 14:14 mansrc/filterBam.1.adoc
-rw-rw-r--     3756 2020-12-09 14:14 mansrc/filterBam.1
-rw-rw-r--     2209 2020-12-10 09:25 mansrc/getSeq.1.adoc
-rw-rw-r--     2965 2020-12-10 09:25 mansrc/getSeq.1
-rw-rw-r--     3202 2020-12-09 14:14 mansrc/homGeneMapping.1.adoc
-rw-rw-r--     4050 2020-12-09 14:14 mansrc/homGeneMapping.1
-rw-rw-r--     3914 2020-12-09 14:14 mansrc/joingenes.1.adoc
-rw-rw-r--     5197 2020-12-09 14:14 mansrc/joingenes.1
-rw-rw-r--     2058 2020-12-10 09:25 mansrc/load2db.1.adoc
-rw-rw-r--     2661 2020-12-10 09:25 mansrc/load2db.1
-rw-rw-r--     2541 2020-12-10 09:25 mansrc/load2sqlitedb.1.adoc
-rw-rw-r--     3167 2020-12-10 09:25 mansrc/load2sqlitedb.1
-rw-rw-r--     2998 2020-09-11 10:44 docs/longrunning-test-CGP.md
-rw-rw-r--       90 2019-05-22 10:34 mansrc/make.doc
-rw-rw-r--   513492 2019-05-22 10:34 docs/MEAposter.pdf
-rw-rw-r--    12020 2019-05-22 10:34 docs/mysql.html
-rw-rw-r--     8157 2020-09-11 10:44 docs/mysql.org
-rw-rw-r--     1213 2019-05-22 10:34 docs/pipeline2gbrowser.txt
-rw-rw-r--   655429 2019-05-22 10:34 docs/pipeline.poster.pdf
-rw-rw-r--     5682 2020-12-10 14:35 mansrc/pp_simScore.1.adoc
-rw-rw-r--     7104 2020-12-10 14:35 mansrc/pp_simScore.1
-rw-rw-r--      675 2019-05-22 10:34 mansrc/prepareAlign.1.adoc
-rw-rw-r--     1139 2019-05-22 10:34 mansrc/prepareAlign.1
-rw-rw-r--     2638 2019-09-13 13:58 docs/REFERENCES.md
-rw-rw-r--    28115 2019-05-22 10:34 docs/retraining.html
-rw-rw-r--    28088 2020-09-11 10:44 docs/RUNNING-AUGUSTUS-IN-CGP-MODE.md
-rw-rw-r--    40502 2019-05-22 10:34 docs/RUNNING-AUGUSTUS.md
-rw-rw-r--   275304 2019-05-22 10:34 docs/tutorial2018/BRAKER_userguide.pdf
-rw-rw-r--    12495 2020-12-09 14:14 docs/tutorial-cgp/cactus.html
-rw-rw-r--     8231 2019-09-13 13:58 docs/tutorial-cgp/de_novo.html
-rw-rw-r--     1498 2020-12-09 14:14 auxprogs/homGeneMapping/Dockerfile
-rw-rw-r--      841 2019-05-22 10:34 docs/espoca/example.fa
-rw-rw-r--    15988 2019-05-22 10:34 docs/tutorial-cgp/hgm.html
-rw-rw-r--    17778 2020-09-11 10:44 docs/tutorial-cgp/index.html
-rw-rw-r--    21103 2019-05-22 10:34 docs/tutorial2018/index.html
-rw-rw-r--     5150 2019-05-22 10:34 docs/tutorial2015/index.html
-rw-rw-r--     6593 2019-05-22 10:34 docs/tutorial/index.html
-rw-rw-r--    19600 2019-05-22 10:34 docs/tutorial2015/ittrain.html
-rw-rw-r--     9341 2019-05-22 10:34 docs/tutorial-cgp/liftover.html
-rw-rw-r--      797 2019-05-22 10:34 examples/utr/make.doc
-rw-rw-r--    15523 2019-05-22 10:34 docs/tutorial2015/ppx.html
-rw-rw-r--    15533 2019-05-22 10:34 docs/tutorial/ppx.html
-rw-rw-r--    23749 2020-09-11 10:44 docs/tutorial2015/prediction.html
-rw-rw-r--    23832 2019-05-22 10:34 docs/tutorial/prediction.html
-rw-rw-r--  2005985 2019-05-22 10:34 docs/tutorial2018/presentation.pdf
-rw-rw-r--    11240 2019-05-22 10:34 docs/tutorial-cgp/rnaseq.html
-rw-rw-r--     8495 2019-05-22 10:34 docs/tutorial-cgp/rnaseq+liftover.html
-rw-rw-r--    14703 2019-05-22 10:34 docs/tutorial2015/scipio.html
-rw-rw-r--    14712 2019-05-22 10:34 docs/tutorial/scipio.html
-rw-rw-r--   253561 2019-05-22 10:34 docs/tutorial2018/STARmanual_2.3.0.1.pdf
-rw-rw-r--    38138 2019-05-22 10:34 docs/tutorial/training.html
-rw-rw-r--    38774 2019-05-22 10:34 docs/tutorial2015/training.html
-rw-rw-r--      249 2019-05-22 10:34 docs/espoca/tree.nwk

First 50 (from 2560) other files:
-rwxrwxr-x    20556 2020-12-11 15:19 scripts/aa2nonred.pl
-rw-rw-r--     1334 2019-05-22 10:34 docs/tutorial/results/abinitio-browser.gff
-rw-rw-r--    24790 2019-05-22 10:34 docs/tutorial/results/abinitio.browser
-rw-rw-r--     5661 2020-12-11 16:32 docs/.ipynb_checkpoints/ABOUT-checkpoint.md
-rwxrwxr-x     3514 2020-12-11 15:19 scripts/add_name_to_gff3.pl
-rw-rw-r--     8386 2019-05-22 10:34 config/species/adorsata/adorsata_parameters.cfg
-rw-rw-r--      810 2019-05-22 10:34 config/species/adorsata/adorsata_weightmatrix.txt
-rw-rw-r--   878932 2019-05-22 10:34 config/species/aedes/aedes_exon_probs.pbl
-rw-rw-r--   140772 2019-05-22 10:34 config/species/aedes/aedes_igenic_probs.pbl
-rw-rw-r--   153809 2019-05-22 10:34 config/species/aedes/aedes_intron_probs.pbl
-rw-rw-r--     3994 2019-05-22 10:34 config/species/aedes/aedes_parameters.cfg
-rw-rw-r--      801 2019-05-22 10:34 config/species/aedes/aedes_weightmatrix.txt
-rw-rw-r--    15833 2020-04-21 16:37 docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl
-rw-rw-r--      642 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/documentation/alignability.html
-rw-rw-r--    39090 2020-09-15 10:33 src/alignment.cc
-rw-rw-r--    14221 2020-09-15 10:33 include/alignment.hh
-rw-rw-r--     1665 2020-09-15 10:33 src/unittests/alignment_unittest.cc
-rw-rw-r--     8476 2019-05-22 10:34 docs/aliit.png
-rw-rw-r--    76122 2019-05-22 10:34 docs/tutorial/data/allest.7M-8M.lst
-rw-rw-r--  1003172 2019-05-22 10:34 docs/tutorial/data/allest.7M-8M.psl
-rw-rw-r--    13040 2019-05-22 10:34 auxprogs/aln2wig/aln2wig.c
-rwxrwxr-x    22136 2020-12-11 17:24 auxprogs/aln2wig/aln2wig
-rwxrwxr-x    22136 2020-12-11 17:24 bin/aln2wig
-rw-rw-r--   216257 2020-12-09 14:14 tests/auxprogs/homGeneMapping/test_files/aln.hal
-rw-rw-r--   108967 2019-05-22 10:34 examples/cgp/aln.maf
-rw-rw-r--   323840 2019-05-22 10:34 config/species/amphimedon/amphimedon_exon_probs.pbl
-rw-rw-r--    45327 2019-05-22 10:34 config/species/amphimedon/amphimedon_igenic_probs.pbl
-rw-rw-r--    59205 2019-05-22 10:34 config/species/amphimedon/amphimedon_intron_probs.pbl
-rw-rw-r--     2377 2019-05-22 10:34 config/species/amphimedon/amphimedon_metapars.cfg
-rw-rw-r--     6892 2019-05-22 10:34 config/species/amphimedon/amphimedon_parameters.cfg
-rw-rw-r--   121407 2019-05-22 10:34 config/species/amphimedon/amphimedon_utr_probs.pbl
-rw-rw-r--      810 2019-05-22 10:34 config/species/amphimedon/amphimedon_weightmatrix.txt
-rw-rw-r--     7399 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc0/Anc0.2bit
-rw-rw-r--    55971 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc0/Anc0.alignability.bw
-rw-rw-r--    34577 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc0.bb
-rw-rw-r--    51787 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc0/Anc0.gc.bw
-rw-rw-r--    11283 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc1/Anc1.2bit
-rw-rw-r--    70561 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc1/Anc1.alignability.bw
-rw-rw-r--    34740 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc1.bb
-rw-rw-r--    66059 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc1/Anc1.gc.bw
-rw-rw-r--    24508 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc2/Anc2.2bit
-rw-rw-r--   100801 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc2/Anc2.alignability.bw
-rw-rw-r--    34977 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc2.bb
-rw-rw-r--    94988 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc2/Anc2.gc.bw
-rw-rw-r--    25961 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc3/Anc3.2bit
-rw-rw-r--   103825 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc3/Anc3.alignability.bw
-rw-rw-r--    34928 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc3.bb
-rw-rw-r--    98391 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc3/Anc3.gc.bw
-rw-rw-r--    30480 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc4/Anc4.2bit
-rw-rw-r--   112879 2019-05-22 10:34 docs/tutorial-cgp/results/vertHub/Anc4/Anc4.alignability.bw
...

A hint: In order to limit the size of this page, in total 2510 archive member files - probably not "information" or "documentation" related - are omitted here. But all those files can be found in the complete docs-related index file or in the originally, by date, by pathname, by filename or by file extension sorted index files (roughly file size each: 0.7 MB).
   MD5 (augustus-3.4.0.tar.gz): 38a66bd3237735220c01eca2347ed8e3
  SHA1 (augustus-3.4.0.tar.gz): a5ec2a39ad42f063e9bab7917e7e11bb453ef9c2
SHA256 (augustus-3.4.0.tar.gz): 246772737862d16755ab0197bb1d4656cafb31db9b38c2cd991a8e8db6f116c8

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