| Name | Size | Date (UTC) | Description | |
|---|---|---|---|---|
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Parent directory | - | 2025-03-15 02:59:52 | |
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actutils.c | 107467 | 2008-10-22 17:19:22 | utility functions for alignments |
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actutils.h | 9154 | 2008-05-02 18:02:39 | utility functions for alignments |
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bandalg0.c | 11834 | 2003-05-30 17:25:35 | File name: bandalgn0.c Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: Functions to perform global linear alignments. |
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bandalg1.c | 7188 | 2003-05-30 17:25:35 | File name: bandalgn1.c Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: Functions to perform global quadratic banded alignments. |
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bandalg2.c | 15590 | 2003-05-30 17:25:35 | File name: Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: Functions to perform both local and global banded alignments. |
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bandalg3.c | 8317 | 2003-05-30 17:25:36 | File name: Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: Functions to perform global banded alignment. |
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bandalg4.c | 23091 | 2003-05-30 17:25:36 | File name: bandalgn.c Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: Functions to perform global banded alignment. |
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bandalg5.c | 9848 | 2003-05-30 17:25:36 | File name: bandalgn.c Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: Functions to perform both local and global banded alignments. |
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bandalgn.c | 35927 | 2003-05-30 17:25:36 | File name: Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: Functions to perform both local and global banded alignments. |
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bandalgn.h | 15396 | 2000-07-26 17:26:25 | File name: Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: prototypes to perform a global gapped alignment on two sequences. |
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blast.c | 410837 | 2008-01-25 21:15:22 | File name: Author: Tom Madden Contents: BLAST functions Detailed Contents: Functions that allocate and deallocate structures used by BLAST. |
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blast.h | 34862 | 2005-12-29 19:56:06 | File name: Author: Tom Madden Contents: prototypes for "public" BLAST functions (ones that other utilitiles may safely call). |
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blast_dust.c | 15343 | 2007-01-23 15:25:22 | file A utility to find low complexity NA regions. This parallels functionality of dust.c from the C toolkit, but without using the structures generated from ASN.1 spec. |
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blast_dust.h | 2173 | 2007-01-23 15:25:22 | file DUST filtering functions. (shouldn't this be merged with blast_filter?) @todo FIXME: include reference? |
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blastconcat.c | 41312 | 2007-05-07 13:30:54 | File name: Author: Karolina Maciag, Aleksandr Morgulis Contents: implementation of functions needed for query multiplexing functionality. |
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blastconcat.h | 2702 | 2004-04-20 14:55:47 | File name: Author: Karolina Maciag, Aleksandr Morgulis Contents: type declarations for query multiplexing code. |
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blastconcatdef.h | 7520 | 2005-09-26 15:02:58 | File name: Author: Karolina Maciag, Aleksandr Morgulis Contents: type definitions and function prototypes for query multiplexing code. |
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blastdef.h | 78000 | 2007-03-13 20:39:58 | File name: Author: Tom Madden Contents: #defines and definitions for structures used by BLAST. |
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blastkar.c | 162466 | 2006-12-14 17:08:19 | File name: Author: Tom Madden Contents: Functions to calculate BLAST probabilities etc. |
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blastkar.h | 26514 | 2005-10-06 12:49:39 | File name: Author: Tom Madden Contents: definitions and prototypes used by blastkar.c to calculate BLAST statistics. |
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blastool.c | 214866 | 2007-03-15 20:39:17 | File name: Author: Tom Madden Contents: Utilities for BLAST |
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blastpri.h | 42554 | 2007-03-13 20:39:04 | File name: Author: Tom Madden Contents: prototypes for "private" BLAST functions, these should not be called by outside utilities. |
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blastutl.c | 383875 | 2010-12-10 18:47:12 | File name: Author: Tom Madden Contents: Utilities for BLAST $Revision: 6.472 $ |
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blfmtutl.c | 45526 | 2012-10-10 14:05:50 | File name: Author: Tom Madden Contents: Utilities for BLAST formatting |
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blfmtutl.h | 7807 | 2006-04-26 12:42:36 | File name: Author: Tom Madden Contents: prototypes and defines for Blast formatting utilities |
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blstxml.asn | 3561 | 2008-08-26 22:25:36 | |
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blstxml.h | 7930 | 2006-09-18 15:20:39 | Automatic header module from ASNTOOL |
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bxmlobj.c | 35747 | 2006-09-18 15:20:39 | |
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bxmlobj.h | 5554 | 2006-09-18 15:20:39 | ifndef _bxmlobj_ |
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csim.c | 40175 | 2003-05-30 17:25:36 | functions for using the sim/sim2 algorithm |
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db_list.h | 4118 | 1997-08-25 18:53:00 | functions used in the sim2 algorithm |
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db_slist.c | 11499 | 2003-05-30 17:25:36 | Example of Skip List source code for C: |
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dotseq.c | 56818 | 2006-07-13 17:16:20 | computes local alignments for dot matrix |
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dotseq.h | 7425 | 2001-08-09 16:33:18 | computes local alignments for dot matrix |
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dust.c | 17449 | 2003-05-30 17:25:36 | a utility to find low complexity NA regions |
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dust.h | 4318 | 1999-08-18 17:57:56 | a utility to find low complexity NA regions |
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falign.c | 73573 | 2003-05-30 17:25:36 | Part 1 of sim2: generate the K best fragment alignments. |
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g_any.c | 12025 | 2003-05-30 17:25:36 | A PACKAGE FOR GLOBALLY ALIGNING TWO SEQUENCES WITHIN AN ARBITRARY REGION: |
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gapxdrop.c | 91161 | 2003-11-07 21:52:52 | File name: Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden [From code originally supplied by Webb Miller's lab]. Contents: Functions to perform a gapped alignment on two sequences. |
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gapxdrop.h | 12562 | 2003-02-28 22:57:24 | File name: Author: Gennadiy Savchuk, Jinqhui Zhang, Tom Madden Contents: prototypes to perform a gapped alignment on two sequences. |
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impatool.c | 24292 | 2006-06-30 18:44:40 | File name: Author: Alejandro Schaffer Contents: utility routines for IMPALA. |
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kappa.c | 106485 | 2013-11-04 15:42:10 | |
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list.h | 4045 | 2000-07-08 20:44:11 | functions used in the sim2 algorithm |
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lnfac.h | 143235 | 1998-06-23 16:41:06 | ifdef WIN16 float |
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lookup.c | 45860 | 2005-07-28 14:57:10 | Functions to store "words" from a query and perform lookups against |
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lookup.h | 19972 | 2007-03-14 16:39:29 | Functions that format traditional BLAST output. |
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mbalign.c | 34605 | 2006-02-02 17:57:34 | Alignment functions for Mega Blast program |
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mbalign.h | 2277 | 2005-05-03 20:29:17 | ifndef __ |
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mblast.c | 161261 | 2006-09-21 13:42:37 | |
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mblast.h | 10598 | 2004-01-16 23:43:44 | File name: Author: Ilya Dondoshansky Contents: prototypes for "public" Mega BLAST functions (ones that other utilitiles may safely call). |
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motif.c | 18963 | 2007-05-07 13:30:54 | sequence motif search functions |
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motif.h | 2781 | 2001-08-08 23:18:57 | sequence motif search functions |
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ncbisam.c | 83709 | 2007-11-06 19:20:06 | Main file for ISAM library |
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ncbisam.h | 14197 | 2006-05-10 20:47:14 | External include file for ISAM library |
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ncbisami.h | 7581 | 2006-05-10 20:47:13 | Internal include file for ISAM library |
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ncbisort.c | 34345 | 2023-11-08 21:26:17 | Main file for SORTing library |
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ncbisort.h | 8284 | 2006-05-10 20:47:17 | External include file for SORTing library |
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ncbisrti.h | 6343 | 2003-12-03 02:10:52 | Internal include file for SORTing library |
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pattern1.c | 64623 | 2023-11-08 21:26:17 | |
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pobutil.c | 52548 | 2007-05-07 13:30:54 | |
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pobutil.h | 6104 | 1998-06-17 22:18:36 | |
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posit.c | 238545 | 2011-10-25 14:33:16 | PUBLIC DOMAIN NOTICE National Center for Biotechnology Information This software/database is a "United States Government Work" under the terms of the United States Copyright Act. |
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posit.h | 15629 | 2011-10-25 14:33:16 | File name: Author: Alejandro Schaffer Contents: header file for position-based BLAST. $Revision: 6.33 $ |
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posit2.c | 16340 | 2006-09-18 20:54:27 | File name: Author: Alejandro Schaffer Contents: utilities for makematrices. $Revision: 6.12 $ |
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profiles.h | 5373 | 2004-09-21 14:45:26 | File name: Author: Alejandro Schaffer Contents: utilities for IMPALA |
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pseed3.c | 74591 | 2017-04-05 04:01:39 | |
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readdb.c | 430556 | 2023-11-08 21:26:17 | Functions to rapidly read databases from files produced by formatdb. |
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readdb.h | 76837 | 2009-01-15 15:20:35 | Functions to rapidly read databases from files produced by formatdb. |
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rpsutil.c | 95423 | 2019-12-16 14:59:41 | Reversed PSI BLAST utilities file |
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rpsutil.h | 14305 | 2003-10-07 15:24:10 | Reversed PSI BLAST utilities file |
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salign.c | 56931 | 2009-01-21 17:09:18 | |
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salign.h | 1324 | 2006-11-21 20:05:35 | Header file containing external functions of salign.c |
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salmedia.h | 2127 | 2006-07-13 17:16:20 | |
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salptool.c | 48950 | 2008-07-07 18:52:31 | |
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salptool.h | 874 | 2008-07-07 18:52:31 | |
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sec.c | 13650 | 2003-05-30 17:25:38 | Part 2 of sim2 - refine the fragment alignments |
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sec.h | 608 | 1997-08-25 18:54:31 | sim_aln.c modified from the sim_aln_old.c. Input to CSIM will be Bioseq object instead of two sequence strings. CSIM is also modified Jinghui Zhang |
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seed.h | 13994 | 2008-01-09 19:04:04 | File name: Author: Alejandro Schaffer Contents: header file for PHI-BLAST and pseed3. |
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seg.c | 39042 | 2003-05-30 17:25:38 | |
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seg.h | 4022 | 2002-03-27 14:41:53 | low-complexity filter 'seg' |
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sim2.c | 4156 | 2003-05-30 17:25:38 | |
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sim3.c | 25505 | 2003-05-30 17:25:38 | compare two very similar sequences with affine gap penalties |
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sim4.c | 87935 | 2003-05-30 17:25:38 | an algorithm to align a cDNA sequence with a genomic sequence. |
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simutil.c | 34379 | 2003-05-30 17:25:38 | functions for using the sim/sim2 algorithm |
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simutil.h | 19046 | 1998-09-09 11:47:43 | Utilities for sim and sim2 algorithm |
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slist.c | 9344 | 2003-05-30 17:25:38 | PUBLIC DOMAIN NOTICE National Center for Biotechnology Information This software/database is a "United States Government Work" under the terms of the United States Copyright Act. |
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spidey.c | 367239 | 2016-09-02 14:57:38 | mrna-to-genomic alignment algorithms and functions |
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spidey.h | 22034 | 2004-03-25 21:20:03 | mrna-to-genomic alignment algorithms and functions |
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splutil.c | 4726 | 2003-05-30 17:25:38 | |
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splutil.h | 1980 | 2000-04-22 15:56:04 | |
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stsutil.c | 36114 | 2003-05-30 17:25:38 | NCBI STS Search Tool utilities |
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stsutil.h | 9360 | 1997-08-25 18:54:52 | Header file for NCBI STS Search Tool utilities |
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suggadj.c | 51221 | 2003-05-30 17:25:38 | |
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suggest.c | 44651 | 2009-04-10 17:22:14 | PUBLIC DOMAIN NOTICE National Center for Biotechnology Information (NCBI) This software/database is a "United States Government Work" under the terms of the United States Copyright Act. |
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suggest.h | 7307 | 2009-04-10 17:22:14 | |
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suggslp.c | 27998 | 2009-04-16 18:35:41 | Implementation of Suggest standalone prediction function. Here it |
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suggslp.h | 2541 | 2009-04-16 18:35:41 | Implementation of standalone Suggest prediction function. |
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taxblast.c | 62939 | 2015-07-06 19:25:47 | Utilities and functions for Tax-Blast program |
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taxblast.h | 3115 | 2002-10-07 19:52:07 | Header file for Tax-Blast program |
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terr.h | 904 | 1997-12-08 22:55:04 | ifndef __MODULE_toasn3__ |
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tfuns.c | 32630 | 2015-08-17 17:15:09 | |
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tfuns.h | 2316 | 2007-10-10 16:10:17 | include <stdio.h> |
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toasn3.c | 188775 | 2016-11-02 23:36:09 | converts a Seq-entry or elements of a Bioseq-set to new Biosource style |
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toasn3.h | 9242 | 2016-07-29 01:49:57 | ifndef _TOASN3_ |
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toporg.c | 203584 | 2017-01-19 22:35:38 | |
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toporg.h | 4065 | 2015-03-02 20:43:47 | ifndef _TOPORG_ |
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urkbias.c | 17622 | 2003-05-30 17:25:38 | codon bias |
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urkbias.h | 3150 | 1998-09-16 17:46:43 | codon bias header |
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urkcnsrt.c | 41098 | 2003-05-30 17:25:38 | consort |
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urkcnsrt.h | 3640 | 1998-10-13 17:16:37 | consort header |
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urkdust.c | 19164 | 2003-05-30 17:25:38 | urkdust |
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urkdust.h | 3845 | 1998-09-16 17:46:44 | urkdust header |
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urkepi.c | 30068 | 2003-05-30 17:25:38 | epi - low complexity |
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urkepi.h | 3474 | 1998-11-16 14:29:51 | epi header |
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urkfltr.c | 12033 | 2003-05-30 17:25:38 | filter |
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urkfltr.h | 3383 | 1998-09-16 17:46:45 | filter header |
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urkgraph.c | 25680 | 2003-05-30 17:25:38 | graph utilities |
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urkgraph.h | 5896 | 1998-09-16 17:46:45 | graph header |
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urkpcc.c | 12855 | 2003-05-30 17:25:38 | coiled-coils |
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urkpcc.h | 3424 | 1998-11-16 14:29:50 | coiled-coil header |
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urkptpf.c | 63911 | 2003-05-30 17:25:38 | patterns and profiles |
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urkptpf.h | 6102 | 1999-07-13 13:07:05 | patterns and profiles header |
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urksigu.c | 5534 | 2003-05-30 17:25:38 | sigme utilities |
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urksigu.h | 2603 | 1998-11-24 15:40:54 | sigme utilities header |
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urktree.c | 34887 | 2003-05-30 17:25:38 | trees |
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urktree.h | 6014 | 1998-09-16 17:46:47 | trees header |
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urkutil.c | 3671 | 2003-05-30 17:25:38 | urk utilities |
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urkutil.h | 2210 | 1999-01-27 15:08:42 | urk utilities header |
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vecscrn.c | 32060 | 2005-12-27 14:46:44 | File name: Author: Tom Madden Contents: functions for Vector screening. |
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vecscrn.h | 8016 | 2000-07-08 20:44:12 | File name: Author: Tom Madden Contents: functions for Vector screening. |
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xmlblast.c | 55637 | 2007-05-07 13:30:54 | Functions to print simplified BLAST output (XML) |
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xmlblast.h | 6930 | 2004-04-29 19:55:35 | Functions to print simplified BLAST output (XML) |