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Contents of Augustus-3.5.0.tar.gz (23 Sep 19:06, 225918930 Bytes)

About: AUGUSTUS is a program to find genes and their structures in one or more genomes.

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Fossies downloads: / linux / misc / Augustus-3.5.0.tar.gz  (tar.bz2|tar.xz|zip)
Fossies services: Doxygen documentation | CLOC analysis | Meta information
Original URL: https://github.com / Gaius-Augustus / Augustus / archive/refs/tags/v3.5.0.tar.gz
Home page: https://bioinf.uni-greifswald.de/webaugustus/
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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, ...):
     4094 2022-09-23 19:06 README.md
      786 2022-09-23 19:06 docs/CDS.sp.README
     2736 2022-09-23 19:06 docs/CHANGE-TREE-PARSER.md
    23798 2022-09-23 19:06 docs/HISTORY.TXT
    23616 2022-09-23 19:06 docs/INSTALL.md
     4968 2022-09-23 19:06 src/LICENSE.TXT
    12670 2022-09-23 19:06 scripts/README.autoAug
     2002 2022-09-23 19:06 docs/README-cgp.md
     7791 2022-09-23 19:06 docs/README_ppsimscore.txt
    18780 2022-09-23 19:06 docs/readme.rnaseq.html
    54374 2022-09-23 19:06 docs/tutorial2018/README_augustus.TXT
     1467 2022-09-23 19:06 auxprogs/bam2wig/README.md
     2281 2022-09-23 19:06 auxprogs/filterBam/README.md
     1905 2022-09-23 19:06 auxprogs/utrrnaseq/README
     2842 2022-09-23 19:06 docs/espoca/README
      545 2022-09-23 19:06 auxprogs/auxBamFilters/README
      754 2022-09-23 19:06 auxprogs/bam2hints/README
      141 2022-09-23 19:06 examples/cgp/README.TXT
     1894 2022-09-23 19:06 examples/autoAug/README.TXT
     4869 2022-09-23 19:06 auxprogs/homGeneMapping/README.TXT


Basic docs (manual pages, PDF-,HTML-,/doc/-files, ...):
     1763 2022-09-23 19:06 Dockerfile
    28115 2022-09-23 19:06 retraining.html
     5661 2022-09-23 19:06 docs/ABOUT.md
      453 2022-09-23 19:06 mansrc/aln2wig.1.adoc
      878 2022-09-23 19:06 mansrc/aln2wig.1
     2977 2022-09-23 19:06 mansrc/augustus.1.adoc
     4039 2022-09-23 19:06 mansrc/augustus.1
     3224 2022-09-23 19:06 docs/AUGUSTUS-ON-WINDOWS.md
     2832 2022-09-23 19:06 mansrc/bam2hints.1.adoc
     3591 2022-09-23 19:06 mansrc/bam2hints.1
      798 2022-09-23 19:06 mansrc/bam2wig.1.adoc
     1225 2022-09-23 19:06 mansrc/bam2wig.1
     8969 2022-09-23 19:06 docs/CDS.sp.pdf
      970 2022-09-23 19:06 mansrc/compileSpliceCands.1.adoc
     1469 2022-09-23 19:06 mansrc/compileSpliceCands.1
      655 2022-09-23 19:06 docs/CONTACT.md
      699 2022-09-23 19:06 mansrc/etraining.1.adoc
     1111 2022-09-23 19:06 mansrc/etraining.1
     4640 2022-09-23 19:06 docs/EXONCAND-MSAS-CGP.md
     1925 2022-09-23 19:06 mansrc/fastBlockSearch.1.adoc
     2446 2022-09-23 19:06 mansrc/fastBlockSearch.1
     3287 2022-09-23 19:06 mansrc/filterBam.1.adoc
     4388 2022-09-23 19:06 mansrc/filterBam.1
     2209 2022-09-23 19:06 mansrc/getSeq.1.adoc
     2965 2022-09-23 19:06 mansrc/getSeq.1
     3202 2022-09-23 19:06 mansrc/homGeneMapping.1.adoc
     4050 2022-09-23 19:06 mansrc/homGeneMapping.1
     3914 2022-09-23 19:06 mansrc/joingenes.1.adoc
     5197 2022-09-23 19:06 mansrc/joingenes.1
     2058 2022-09-23 19:06 mansrc/load2db.1.adoc
     2661 2022-09-23 19:06 mansrc/load2db.1
     2541 2022-09-23 19:06 mansrc/load2sqlitedb.1.adoc
     3167 2022-09-23 19:06 mansrc/load2sqlitedb.1
     2998 2022-09-23 19:06 docs/longrunning-test-CGP.md
       90 2022-09-23 19:06 mansrc/make.doc
   513492 2022-09-23 19:06 docs/MEAposter.pdf
    11260 2022-09-23 19:06 docs/mysql.html
     7728 2022-09-23 19:06 docs/mysql.org
     1213 2022-09-23 19:06 docs/pipeline2gbrowser.txt
   655429 2022-09-23 19:06 docs/pipeline.poster.pdf
     5682 2022-09-23 19:06 mansrc/pp_simScore.1.adoc
     7104 2022-09-23 19:06 mansrc/pp_simScore.1
      675 2022-09-23 19:06 mansrc/prepareAlign.1.adoc
     1139 2022-09-23 19:06 mansrc/prepareAlign.1
     2638 2022-09-23 19:06 docs/REFERENCES.md
    28088 2022-09-23 19:06 docs/RUNNING-AUGUSTUS-IN-CGP-MODE.md
    40600 2022-09-23 19:06 docs/RUNNING-AUGUSTUS.md
   275304 2022-09-23 19:06 docs/tutorial2018/BRAKER_userguide.pdf
    12495 2022-09-23 19:06 docs/tutorial-cgp/cactus.html
     8231 2022-09-23 19:06 docs/tutorial-cgp/de_novo.html
     1488 2022-09-23 19:06 auxprogs/homGeneMapping/Dockerfile
      841 2022-09-23 19:06 docs/espoca/example.fa
    15988 2022-09-23 19:06 docs/tutorial-cgp/hgm.html
    17778 2022-09-23 19:06 docs/tutorial-cgp/index.html
    21103 2022-09-23 19:06 docs/tutorial2018/index.html
     5150 2022-09-23 19:06 docs/tutorial2015/index.html
     6593 2022-09-23 19:06 docs/tutorial/index.html
    19600 2022-09-23 19:06 docs/tutorial2015/ittrain.html
     9341 2022-09-23 19:06 docs/tutorial-cgp/liftover.html
      797 2022-09-23 19:06 examples/utr/make.doc
    15523 2022-09-23 19:06 docs/tutorial2015/ppx.html
    15533 2022-09-23 19:06 docs/tutorial/ppx.html
    23749 2022-09-23 19:06 docs/tutorial2015/prediction.html
    23832 2022-09-23 19:06 docs/tutorial/prediction.html
  2005985 2022-09-23 19:06 docs/tutorial2018/presentation.pdf
    11240 2022-09-23 19:06 docs/tutorial-cgp/rnaseq.html
     8495 2022-09-23 19:06 docs/tutorial-cgp/rnaseq+liftover.html
    14703 2022-09-23 19:06 docs/tutorial2015/scipio.html
    14712 2022-09-23 19:06 docs/tutorial/scipio.html
   253561 2022-09-23 19:06 docs/tutorial2018/STARmanual_2.3.0.1.pdf
    38138 2022-09-23 19:06 docs/tutorial/training.html
    38774 2022-09-23 19:06 docs/tutorial2015/training.html
      249 2022-09-23 19:06 docs/espoca/tree.nwk


First 50 (from 2500) other files:
    20556 2022-09-23 19:06 scripts/aa2nonred.pl
     1334 2022-09-23 19:06 docs/tutorial/results/abinitio-browser.gff
    24790 2022-09-23 19:06 docs/tutorial/results/abinitio.browser
     3528 2022-09-23 19:06 scripts/add_name_to_gff3.pl
     8386 2022-09-23 19:06 config/species/adorsata/adorsata_parameters.cfg
      810 2022-09-23 19:06 config/species/adorsata/adorsata_weightmatrix.txt
   878932 2022-09-23 19:06 config/species/aedes/aedes_exon_probs.pbl
   140772 2022-09-23 19:06 config/species/aedes/aedes_igenic_probs.pbl
   153809 2022-09-23 19:06 config/species/aedes/aedes_intron_probs.pbl
     3994 2022-09-23 19:06 config/species/aedes/aedes_parameters.cfg
      801 2022-09-23 19:06 config/species/aedes/aedes_weightmatrix.txt
    15833 2022-09-23 19:06 docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl
      642 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/documentation/alignability.html
    39090 2022-09-23 19:06 src/alignment.cc
    14221 2022-09-23 19:06 include/alignment.hh
     1665 2022-09-23 19:06 src/unittests/alignment_unittest.cc
     8476 2022-09-23 19:06 docs/aliit.png
    76122 2022-09-23 19:06 docs/tutorial/data/allest.7M-8M.lst
  1003172 2022-09-23 19:06 docs/tutorial/data/allest.7M-8M.psl
    12275 2022-09-23 19:06 auxprogs/aln2wig/aln2wig.c
   216257 2022-09-23 19:06 tests/short/auxprogs/homgenemapping/test_files/aln.hal
   108967 2022-09-23 19:06 examples/cgp/aln.maf
   323840 2022-09-23 19:06 config/species/amphimedon/amphimedon_exon_probs.pbl
    45327 2022-09-23 19:06 config/species/amphimedon/amphimedon_igenic_probs.pbl
    59205 2022-09-23 19:06 config/species/amphimedon/amphimedon_intron_probs.pbl
     2377 2022-09-23 19:06 config/species/amphimedon/amphimedon_metapars.cfg
     6892 2022-09-23 19:06 config/species/amphimedon/amphimedon_parameters.cfg
   121407 2022-09-23 19:06 config/species/amphimedon/amphimedon_utr_probs.pbl
      810 2022-09-23 19:06 config/species/amphimedon/amphimedon_weightmatrix.txt
     7399 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc0/Anc0.2bit
    55971 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc0/Anc0.alignability.bw
    34577 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc0.bb
    51787 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc0/Anc0.gc.bw
    11283 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc1/Anc1.2bit
    70561 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc1/Anc1.alignability.bw
    34740 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc1.bb
    66059 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc1/Anc1.gc.bw
    24508 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc2/Anc2.2bit
   100801 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc2/Anc2.alignability.bw
    34977 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc2.bb
    94988 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc2/Anc2.gc.bw
    25961 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc3/Anc3.2bit
   103825 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc3/Anc3.alignability.bw
    34928 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc3.bb
    98391 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc3/Anc3.gc.bw
    30480 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc4/Anc4.2bit
   112879 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc4/Anc4.alignability.bw
    35115 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/liftoverbed/refseq/hg38/Anc4.bb
   114917 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc4/Anc4.gc.bw
    47067 2022-09-23 19:06 docs/tutorial-cgp/results/vertHub/Anc5/Anc5.2bit
...
A hint: In order to limit the size of this page, in total 2450 archive member files 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-3.5.0.tar.gz): 2d2c9916c5389a82d1c86e8ea0e7509c
  SHA1 (Augustus-3.5.0.tar.gz): 6c514bf334ba1d4c928b89c79beb1e311667072c
SHA256 (Augustus-3.5.0.tar.gz): 5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686
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