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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
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--    18695 2016-03-29 16:38 HISTORY.TXT
-rw-rw-r--    20859 2016-03-14 17:26 README-cgp.txt
-rw-rw-r--    53244 2016-03-30 16:22 README.TXT
-rw-r--r--      786 2015-04-24 14:23 docs/CDS.sp.README
-rw-rw-r--     4971 2015-10-14 10:06 src/LICENCE.TXT
-rwxr-xr-x    12539 2015-04-24 14:23 scripts/README.autoAug
-rw-r--r--    18780 2015-04-24 14:23 docs/readme.rnaseq.html
-rw-r--r--      545 2015-04-24 14:24 auxprogs/auxBamFilters/README
-rw-rw-r--     1855 2015-10-14 10:06 auxprogs/bam2hints/README
-rw-rw-r--     3355 2015-10-16 16:56 auxprogs/filterBam/README
-rw-r--r--     1894 2015-04-24 14:23 examples/autoAug/README.TXT
-rw-r--r--     2175 2015-04-24 14:24 auxprogs/homGeneMapping/README.TXT
-rw-r--r--      664 2015-09-25 16:44 auxprogs/bam2wig/README.txt
-rw-rw-r--      141 2015-09-21 09:44 examples/cgp/README.TXT
-rw-rw-r--      813 2016-03-14 17:26 auxprogs/homGeneMapping/TODO.TXT
-rw-r--r--      726 2015-04-24 14:24 config/species/wheat/README.txt
-rw-rw-r--      123 2015-09-25 16:51 docs/tutorial2015/results/README.TXT
-rwxr-xr-x     2258 2015-04-24 14:24 config/species/camponotus_floridanus/README.TXT
-rwxr-xr-x      252 2015-04-24 14:24 config/species/s_aureus/README.TXT
-rwxr-xr-x     2746 2015-04-24 14:24 config/species/rice/README.TXT
-rwxr-xr-x      608 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/README.TXT
-rwxr-xr-x      772 2015-04-24 14:23 config/species/pneumocystis/README.TXT
-rwxr-xr-x      897 2015-04-24 14:24 config/species/human/README.TXT
-rwxr-xr-x      904 2015-04-24 14:23 config/species/zebrafish/README.TXT
-rwxr-xr-x      999 2015-04-24 14:24 config/species/chicken/README.TXT

Basic docs (manual pages, PDF-,HTML-,/doc/-files, ...):
-rw-r--r--    28114 2015-09-25 12:29 retraining.html
-rw-r--r--     8969 2015-04-24 14:23 docs/CDS.sp.pdf
-rw-r--r--   513492 2015-04-24 14:23 docs/MEAposter.pdf
-rw-r--r--    12020 2015-04-24 14:23 docs/mysql.html
-rw-r--r--     8157 2015-04-24 14:23 docs/mysql.org
-rw-r--r--     1213 2015-04-24 14:23 docs/pipeline2gbrowser.txt
-rw-r--r--   655429 2015-04-24 14:23 docs/pipeline.poster.pdf
-rw-r--r--     6561 2015-04-24 14:23 docs/tutorial/index.html
-rw-rw-r--     5152 2015-07-16 12:38 docs/tutorial2015/index.html
-rw-rw-r--    19601 2015-07-22 11:21 docs/tutorial2015/ittrain.html
-rw-r--r--    15533 2015-04-24 14:23 docs/tutorial/ppx.html
-rw-rw-r--    15523 2015-07-16 12:38 docs/tutorial2015/ppx.html
-rw-r--r--    23744 2015-04-24 14:23 docs/tutorial/prediction.html
-rw-rw-r--    23734 2015-07-16 12:38 docs/tutorial2015/prediction.html
-rw-r--r--    14713 2015-04-24 14:23 docs/tutorial/scipio.html
-rw-rw-r--    14703 2015-07-16 12:38 docs/tutorial2015/scipio.html
-rw-r--r--    38137 2015-04-24 14:23 docs/tutorial/training.html
-rw-rw-r--    38773 2015-07-16 12:38 docs/tutorial2015/training.html
-rw-r--r--     1334 2015-04-24 14:23 docs/tutorial/results/abinitio-browser.gff
-rw-r--r--    24790 2015-04-24 14:23 docs/tutorial/results/abinitio.browser
-rw-r--r--    76122 2015-04-24 14:23 docs/tutorial/data/allest.7M-8M.lst
-rw-r--r--  1003172 2015-04-24 14:23 docs/tutorial/data/allest.7M-8M.psl
-rw-r--r--    36426 2015-04-24 14:23 docs/tutorial/data/augustus.abinitio.aa
-rw-r--r--   146508 2015-04-24 14:23 docs/tutorial/results/augustus.abinitio.gff
-rw-r--r--  1336497 2015-04-24 14:23 docs/tutorial/results/augustus.hints.gff
-rw-r--r--     2713 2015-04-24 14:23 docs/tutorial/results/augustus-ppx.browser
-rw-r--r--     9314 2015-04-24 14:23 docs/tutorial/results/augustus-ppx.gff
-rw-r--r--      174 2015-04-24 14:23 docs/tutorial/results/badgenes.lst
-rw-r--r--   749684 2015-04-24 14:23 docs/tutorial/data/chr2R.2M-7M.aa
-rw-r--r--  5100007 2015-04-24 14:23 docs/tutorial/data/chr2R.2M-7M.fa
-rw-r--r--  4115265 2015-04-24 14:23 docs/tutorial/data/chr2R.7M-8M.wig
-rw-r--r-- 21569650 2015-04-24 14:23 docs/tutorial/data/chr2R.fa
-rw-r--r--  2025027 2015-04-24 14:23 docs/tutorial/data/chr3.42M.fa
-rw-r--r--  2025029 2015-04-24 14:23 docs/tutorial/data/chr4.103M.fa
-rw-r--r--  2025029 2015-04-24 14:23 docs/tutorial/data/chr5.124M.fa
-rw-r--r--  3553399 2015-04-24 14:23 docs/tutorial/data/est.chr2R.7M-8M.fa
-rw-r--r--   938516 2015-04-24 14:23 docs/tutorial/results/est.f.psl
-rw-r--r--  1146203 2015-04-24 14:23 docs/tutorial/data/est.psl
-rw-r--r--  4335584 2015-04-24 14:23 docs/tutorial/results/genes.gb
-rw-r--r--   822894 2015-04-24 14:23 docs/tutorial/results/genes.gb.test
-rw-r--r--  3512690 2015-04-24 14:23 docs/tutorial/results/genes.gb.train
-rw-r--r--  1224821 2015-04-24 14:23 docs/tutorial/results/hints.est.gff
-rw-r--r--  2515815 2015-04-24 14:23 docs/tutorial/results/hints.gff
-rw-r--r--  1240971 2015-04-24 14:23 docs/tutorial/results/hints.rnaseq.ep.gff
-rw-r--r--    50023 2015-04-24 14:23 docs/tutorial/data/hints.rnaseq.intron.gff
-rw-r--r--   503483 2015-04-24 14:24 config/species/human/human_exon_probs.pbl
-rw-r--r--    65030 2015-04-24 14:24 config/species/human/human_igenic_probs.pbl
-rw-r--r--   444544 2015-04-24 14:24 config/species/human/human_intron_probs.pbl
-rw-r--r--    14423 2015-04-24 14:24 config/species/human/human_trans_shadow_partial_utr.pbl
-rw-r--r--   138309 2015-04-24 14:24 config/species/human/human_utr_probs.pbl
-rw-r--r--      806 2015-04-24 14:24 config/species/human/human_weightmatrix.txt
-rw-r--r--     3758 2015-04-24 14:23 docs/tutorial/results/output-abinitio.gff
-rw-r--r--     2713 2015-04-24 14:23 docs/tutorial/results/output-browser.gff
-rw-r--r--     9348 2015-04-24 14:23 docs/tutorial/results/output.gff
-rw-r--r--      925 2015-04-24 14:23 docs/tutorial/results/PF00171.fbs.txt
-rw-r--r-- 36389290 2015-04-24 14:23 docs/tutorial/data/PF00171_full.txt
-rw-r--r--    29831 2015-04-24 14:23 docs/tutorial/results/PF00171.prfl
-rw-r--r--   100438 2015-04-24 14:23 docs/tutorial/results/PF00171_seed.blocks.txt
-rw-r--r--    76877 2015-04-24 14:23 docs/tutorial/data/PF00171_seed.txt
-rw-r--r--      758 2015-04-24 14:23 docs/tutorial/results/PF00225.fbs.txt
-rw-r--r--  1087383 2015-04-24 14:23 docs/tutorial/data/PF00225_full.blocks.txt
-rw-r--r--  7246393 2015-04-24 14:23 docs/tutorial/data/PF00225_full.txt
-rw-r--r--    25958 2015-04-24 14:23 docs/tutorial/results/PF00225.prfl
-rw-r--r--    60369 2015-04-24 14:23 docs/tutorial/results/PF00225_seed.blocks.txt
-rw-r--r--    25957 2015-04-24 14:23 docs/tutorial/results/PF00225_seed.prfl
-rw-r--r--    58429 2015-04-24 14:23 docs/tutorial/data/PF00225_seed.txt
-rw-r--r--      624 2015-04-24 14:23 docs/tutorial/results/PR00249.fbs.txt
-rw-r--r--    29167 2015-04-24 14:23 docs/tutorial/results/PR00249.prfl
-rw-r--r--    40861 2015-04-24 14:23 docs/tutorial/data/PRINTS-example.txt
-rw-r--r--   817426 2015-04-24 14:23 docs/tutorial/results/prot.vs.genome.psl
-rw-rw-r-- 62699070 2015-07-16 12:38 docs/tutorial2015/data/rnaseq1.fq
-rw-rw-r-- 62699070 2015-07-16 12:38 docs/tutorial2015/data/rnaseq2.fq
-rw-r--r--   434746 2015-04-24 14:23 docs/tutorial/results/scipio.browser
-rw-r--r--   434578 2015-04-24 14:23 docs/tutorial/results/scipio.gff
-rw-r--r-- 15961010 2015-04-24 14:23 docs/tutorial/results/scipio.yaml
-rw-r--r--  5099092 2015-04-24 14:23 docs/tutorial/data/sequence.fasta
-rw-r--r--    55086 2015-04-24 14:23 docs/tutorial/results/withhints.browser

First 50 (from 1121) other files:
-rw-r--r--     8388 2015-04-24 14:24 config/species/adorsata/adorsata_parameters.cfg
-rw-r--r--      810 2015-04-24 14:24 config/species/adorsata/adorsata_weightmatrix.txt
-rw-r--r--   878932 2015-04-24 14:23 config/species/aedes/aedes_exon_probs.pbl
-rw-r--r--   140772 2015-04-24 14:23 config/species/aedes/aedes_igenic_probs.pbl
-rw-r--r--   153809 2015-04-24 14:23 config/species/aedes/aedes_intron_probs.pbl
-rw-r--r--     3995 2015-04-24 14:23 config/species/aedes/aedes_parameters.cfg
-rw-r--r--      801 2015-04-24 14:23 config/species/aedes/aedes_weightmatrix.txt
-rw-rw-r--    36161 2016-03-14 17:26 src/alignment.cc
-rw-rw-r--     9360 2015-07-16 12:38 include/alignment.hh
-rw-r--r--     8476 2015-04-24 14:23 docs/aliit.png
-rw-rw-r--    13016 2015-10-16 16:56 auxprogs/aln2wig/aln2wig.c
-rw-rw-r--    59904 2016-03-30 15:59 auxprogs/aln2wig/aln2wig.o
-rwxrwxr-x    39376 2016-03-30 17:19 auxprogs/aln2wig/aln2wig
-rwxr-xr-x   216257 2015-04-24 14:24 auxprogs/homGeneMapping/examples/aln.hal
-rw-r--r--   108967 2015-04-24 14:23 examples/cgp/aln.maf
-rw-r--r--   323840 2015-04-24 14:24 config/species/amphimedon/amphimedon_exon_probs.pbl
-rw-r--r--    45327 2015-04-24 14:24 config/species/amphimedon/amphimedon_igenic_probs.pbl
-rw-r--r--    59205 2015-04-24 14:24 config/species/amphimedon/amphimedon_intron_probs.pbl
-rw-r--r--     2377 2015-04-24 14:24 config/species/amphimedon/amphimedon_metapars.cfg
-rw-r--r--     6894 2015-04-24 14:24 config/species/amphimedon/amphimedon_parameters.cfg
-rw-r--r--   121407 2015-04-24 14:24 config/species/amphimedon/amphimedon_utr_probs.pbl
-rw-r--r--      810 2015-04-24 14:24 config/species/amphimedon/amphimedon_weightmatrix.txt
-rw-r--r--   244514 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_exon_probs.pbl
-rw-r--r--    32498 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_igenic_probs.pbl
-rw-r--r--   351321 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_intron_probs.pbl
-rw-r--r--     2057 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.cfg
-rw-r--r--     1355 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_metapars.utr.cfg
-rw-r--r--     7371 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_parameters.cfg
-rw-r--r--      810 2015-04-24 14:24 config/species/ancylostoma_ceylanicum/ancylostoma_ceylanicum_weightmatrix.txt
-rw-r--r--  1012355 2015-04-24 14:24 config/species/anidulans/anidulans_exon_probs.pbl
-rw-r--r--   140203 2015-04-24 14:24 config/species/anidulans/anidulans_igenic_probs.pbl
-rw-r--r--   176440 2015-04-24 14:24 config/species/anidulans/anidulans_intron_probs.pbl
-rw-r--r--     4121 2015-04-24 14:24 config/species/anidulans/anidulans_parameters.cfg
-rw-r--r--      800 2015-04-24 14:24 config/species/anidulans/anidulans_weightmatrix.txt
-rw-r--r--   433381 2015-04-24 14:24 config/species/arabidopsis/arabidopsis_exon_probs.pbl
-rw-r--r--    46188 2015-04-24 14:24 config/species/arabidopsis/arabidopsis_igenic_probs.pbl
-rw-r--r--   167119 2015-04-24 14:24 config/species/arabidopsis/arabidopsis_intron_probs.pbl
-rw-r--r--     6101 2015-04-24 14:24 config/species/arabidopsis/arabidopsis_parameters.cfg
-rw-r--r--    93284 2015-04-24 14:24 config/species/arabidopsis/arabidopsis_utr_probs.pbl
-rw-r--r--      801 2015-04-24 14:24 config/species/arabidopsis/arabidopsis_weightmatrix.txt
-rw-r--r--   974446 2015-04-24 14:24 config/species/aspergillus_fumigatus/aspergillus_fumigatus_exon_probs.pbl
-rw-r--r--   138249 2015-04-24 14:24 config/species/aspergillus_fumigatus/aspergillus_fumigatus_igenic_probs.pbl
-rw-r--r--   178715 2015-04-24 14:24 config/species/aspergillus_fumigatus/aspergillus_fumigatus_intron_probs.pbl
-rw-r--r--     1860 2015-04-24 14:24 config/species/aspergillus_fumigatus/aspergillus_fumigatus_metapars.cfg
-rw-r--r--     6839 2015-04-24 14:24 config/species/aspergillus_fumigatus/aspergillus_fumigatus_parameters.cfg
-rw-r--r--      810 2015-04-24 14:24 config/species/aspergillus_fumigatus/aspergillus_fumigatus_weightmatrix.txt
-rw-r--r--   320412 2015-04-24 14:23 config/species/aspergillus_nidulans/aspergillus_nidulans_exon_probs.pbl
-rw-r--r--    46658 2015-04-24 14:23 config/species/aspergillus_nidulans/aspergillus_nidulans_igenic_probs.pbl
-rw-r--r--    52240 2015-04-24 14:23 config/species/aspergillus_nidulans/aspergillus_nidulans_intron_probs.pbl
-rw-r--r--     1860 2015-04-24 14:23 config/species/aspergillus_nidulans/aspergillus_nidulans_metapars.cfg
...

A hint: In order to limit the size of this page, in total 1071 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: 0.3 MB).
   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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