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Rev Chgset Date Author Log Message
(edit) @265 [265] 09/17/09 14:28:34 cholt set filter=seg for blastx instead of wordmask=seg, gives better …
(edit) @260 [260] 09/09/09 13:38:19 cholt made indexing search less IO intensive
(edit) @259 [259] 09/08/09 16:43:05 cholt mpi_iprscan more maker like behavior
(edit) @258 [258] 09/08/09 11:32:56 cholt better iprscan wrapper
(edit) @256 [256] 09/04/09 10:45:29 cholt Update tiers
(edit) @255 [255] 09/04/09 09:54:32 cholt update how chunks and tiers work to accept chunk type
(edit) @254 [254] 09/04/09 09:46:41 cholt iprscan and gff3_merge and fastamerge update
(edit) @252 [252] 09/02/09 13:45:06 cholt IO prompt
(edit) @250 [250] 09/01/09 11:26:15 cholt fix run_all method and next_chunk method in MpiTiers?
(edit) @249 [249] 08/31/09 17:07:51 cholt index error fixes
(edit) @248 [248] 08/31/09 08:34:40 cholt weird index error and blast merge error
(edit) @247 [247] 08/27/09 12:41:35 cholt fix weird merging error
(edit) @246 [246] 08/25/09 12:23:02 cholt fix genemark bug
(edit) @245 [245] 08/24/09 17:03:49 cholt fgenesh fix
(edit) @244 [244] 08/21/09 16:52:11 cholt bug in repeat mask cause by prok upgrade
(edit) @243 [243] 08/21/09 10:05:33 cholt prokaryote maker updae
(edit) @242 [242] 08/18/09 14:25:27 cholt prokaryote maker
(edit) @240 [240] 08/03/09 13:05:45 cholt fix nfs lock
(edit) @239 [239] 07/27/09 16:04:03 cholt GI updated
(edit) @237 [237] 07/27/09 16:01:57 cholt GI updated
(edit) @235 [235] 07/14/09 23:23:44 cholt fixed for abinit to pred_gff
(edit) @232 [232] 07/14/09 11:37:18 cholt quick repeatmask
(edit) @231 [231] 07/14/09 11:36:10 cholt fix formatdb
(edit) @229 [229] 07/12/09 20:49:05 cholt gmod build
(edit) @228 [228] 07/07/09 15:20:38 cholt update mpi_iprscan
(edit) @225 [225] 06/22/09 16:20:18 cholt fix more mpi_iprscan
(edit) @222 [222] 06/22/09 12:34:39 cholt update maker
(edit) @221 [221] 06/22/09 12:33:44 cholt mpi_iprscan added
(edit) @220 [220] 06/12/09 16:57:31 hao AED is corrected in evaluator and no more nearly infinite loop~
(edit) @219 [219] 06/12/09 15:55:52 hao greatly changed evaluator AED calculated algorithm to make it fasta, but …
(edit) @218 [218] 06/03/09 11:46:38 hao fixed an evaluator bug
(edit) @216 [216] 05/13/09 09:32:23 cholt augustus update
(edit) @215 [215] 05/13/09 09:17:32 cholt augustus fix
(edit) @214 [214] 05/12/09 17:00:43 cholt fix for new augustus output
(edit) @211 [211] 04/30/09 14:02:43 cholt added better genemark support
(edit) @209 [209] 04/28/09 15:01:45 cholt lock file update
(edit) @207 [207] 04/28/09 14:58:46 cholt fix error checking in widgets
(edit) @203 [203] 04/14/09 14:54:26 hao fixed a evaluator bug in pseudo_hit.pm
(edit) @202 [202] 04/14/09 12:53:07 cholt fixed some gff3 issues
(edit) @200 [200] 04/13/09 16:52:41 hao fixed a bug in evaluator
(edit) @198 [198] 04/08/09 14:42:34 cholt Changed back to three control files, and added mpi_evaluator
(edit) @197 [197] 04/08/09 13:54:07 cholt mapping formard now works
(edit) @195 [195] 04/07/09 16:36:40 cholt fix dumper GFFDB, and added again option to maker
(edit) @194 [194] 04/07/09 15:36:10 cholt fix GFF dumper error, fix bad CDS error, fix change gffdb error, fix uniw …
(edit) @193 [193] 04/04/09 12:43:21 cholt fix UTR join
(edit) @191 [191] 04/02/09 00:18:17 cholt fix run_log
(edit) @190 [190] 04/01/09 23:40:44 cholt improve runlog to always remove temp_dirs
(edit) @189 [189] 04/01/09 23:32:59 cholt fix run_log not deleting error
(edit) @188 [188] 04/01/09 15:42:04 cholt fix auto_annotator predictions not moving forward bug
(edit) @187 [187] 04/01/09 14:59:13 cholt fix auto_annotator bug
(edit) @186 [186] 04/01/09 14:31:37 cholt fix all_preds in evidence and changed how clusters are made for …
(edit) @185 [185] 03/31/09 16:14:50 cholt fix auto_annotator error and control files error and updarte gff3.tiers
(edit) @184 [184] 03/31/09 15:38:02 cholt fix bug in control file proccessing
(edit) @183 [183] 03/31/09 15:17:40 cholt map names forward, CDS competition on opposite strands accounted for
(edit) @182 [182] 03/26/09 22:50:47 cholt augustus bug fix and gff3.tiers edit
(edit) @181 [181] 03/26/09 16:44:29 cholt update maker to accept min protein lengths
(edit) @179 [179] 03/25/09 11:14:17 cholt temporary fix to GFFDB.pm names
(edit) @173 [173] 03/24/09 15:08:16 cholt update README
(edit) @172 [172] 03/23/09 23:09:11 cholt added genemark
(edit) @171 [171] 03/20/09 15:49:38 cholt added genemark
(edit) @170 [170] 03/20/09 10:37:57 hao fixed another bug in evaluator in passing parameters
(edit) @169 [169] 03/19/09 17:09:08 cholt fix evidence merge bug
(edit) @168 [168] 03/19/09 16:55:49 cholt added check pn abinit overhang
(edit) @167 [167] 03/19/09 15:38:00 hao Fix a minor bug in evaluate.pm
(edit) @166 [166] 03/18/09 14:45:05 cholt fix B < E error and many more
(edit) @165 [165] 03/18/09 14:09:53 cholt fix evidence merge error
(edit) @164 [164] 03/17/09 17:15:26 cholt fix gff3 passthrough error
(edit) @163 [163] 03/17/09 16:33:56 cholt fix hsp duplication error
(edit) @162 [162] 03/17/09 13:31:36 cholt evaluator ok to run in new maker
(edit) @161 [161] 03/17/09 11:17:17 cholt xAED implemented
(edit) @160 [160] 03/16/09 14:18:16 cholt Maker Updates for OOmycete genome, clone hsps, hits in join.pm
(edit) @159 [159] 03/09/09 00:50:16 cholt maker update for all oomycete
(edit) @158 [158] 03/09/09 00:49:43 cholt maker update with oomycete genome
(edit) @157 [157] 02/25/09 15:03:14 hao --
(edit) @156 [156] 02/20/09 17:43:22 hao Fix no evaluator output bug
(edit) @155 [155] 02/20/09 13:55:44 cholt fix fail on fathom disabled
(edit) @153 [153] 02/20/09 13:40:05 cholt fathom enabled
(edit) @152 [152] 02/20/09 12:42:04 cholt evaluator active
(edit) @151 [151] 02/20/09 12:38:14 cholt maker update CDS has stop codon and other opts
(edit) @150 [150] 02/10/09 13:58:36 hao --
(edit) @147 [147] 02/10/09 12:02:11 hao --
(edit) @146 [146] 02/09/09 16:49:11 cholt temporarily disabled evaluator AED
(edit) @145 [145] 02/07/09 00:29:07 cholt fix single exon est2genome error
(edit) @144 [144] 02/06/09 23:23:19 cholt mpi maker updated
(edit) @143 [143] 02/06/09 17:02:43 cholt fix weird fasta errors
(edit) @142 [142] 02/02/09 17:48:46 hao removed UTR before generating snap-backwards
(edit) @141 [141] 02/02/09 16:23:00 hao added snap-backwards score
(edit) @140 [140] 01/30/09 14:40:35 hao --
(edit) @139 [139] 01/28/09 12:54:41 cholt fix gff3 parsing error and blast empty error
(edit) @138 [138] 01/28/09 10:43:01 hao --
(edit) @137 [137] 01/27/09 16:59:05 cholt no valid contexrts error fix
(edit) @136 [136] 01/27/09 15:52:17 hao added pseudo hit feature
(edit) @135 [135] 01/26/09 19:19:30 hao --
(edit) @134 [134] 01/25/09 11:32:42 hao Added new AED feature
(edit) @133 [133] 01/23/09 17:02:42 cholt ignore contig line in all gff3
(edit) @132 [132] 01/23/09 16:58:10 cholt fix annotation passthrough
(edit) @131 [131] 01/23/09 16:22:26 cholt fix fasta index error
(edit) @130 [130] 01/23/09 14:19:44 cholt fix get_selected_type function errors
(edit) @129 [129] 01/23/09 13:00:25 cholt remove redundant files
(edit) @128 [128] 01/23/09 12:59:29 cholt missing MakerChunk?
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