treangen's sequence [86 articles] Export

Recent papers added to treangen's library classified by the tag sequence. You can also see everyone's sequence.

	DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 66. by Amarendran Subramanian, Jan W. Menkhoff, Michael Kaufmann, Burkhard Morgenstern posted to alignment local multiple segment sequence software by treangen on 2008-12-12 09:21:24 as along with 3 people walshtp BioNica moborg
	Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. [My Copy] Nucleic acids research (4 December 2008) by Yue Lu, Sing-Hoi H. Sze posted to accuracy alignment jctalk multiple nralign sequence software by treangen on 2008-12-11 15:49:48 as along with 6 people n00c zwang zanexu dakelley gjuggler nuin
	MAFFT version 5: improvement in accuracy of multiple sequence alignment. [My Copy] Nucleic acids research, Vol. 33, No. 2. (2005), pp. 511-518. by K. Katoh, K. Kuma, H. Toh, T. Miyata posted to alignment msa multiple sequence software by treangen on 2008-12-11 14:22:50 as along with 8 people and 1 group hryk BioNica druvus CharlesM caporaso rabio timflutre urgi biomedical-nlp
	Recent developments in the MAFFT multiple sequence alignment program. [My Copy] Briefings in bioinformatics (27 March 2008) by Kazutaka Katoh, Hiroyuki Toh posted to alignment msa multiple sequence software by treangen on 2008-12-11 14:22:29 as along with 3 people BioNica urgi timflutre
	Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees [My Copy] Molecular Biology and Evolution, Vol. 23, No. 11. (November 2006), pp. 2090-2100. by Cantarel, L. Brandi, Morrison, G. Hilary, Pearson, William posted to 2006 accuracy phylogenetic sequence similarity trees by treangen on 2008-12-03 15:48:47 as along with 4 people druvus gjuggler mblwhoi ArtemPankin
	XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (07 October 2008), 420. by Daniel Frank posted to metagenomics phylogenetic sequence software xplorseq by treangen on 2008-11-29 17:47:45 as along with 5 people and 3 groups vaulot jlgreen Thaverkamp ojabado nuin Papers recommended by the Roscoff Plankton Group Microbial-Ecology iSEEM
	SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics [My Copy] BMC Evolutionary Biology, Vol. 7, No. Suppl 1. (2007) by Beatrice Roure, Naiara R. Ezpeleta, Herve Philippe posted to concatenation genome phylogenomics sequence software by treangen on 2008-11-27 19:39:47 as along with 7 people calderonv natstreet druvus operon aprasad akifumi dmp
	The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. [My Copy] DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 15, No. 4. (August 2008), pp. 185-199. by K. Nakayama, A. Yamashita, K. Kurokawa, et al.T. Morimoto, M. Ogawa, M. Fukuhara, H. Urakami, M. Ohnishi, I. Uchiyama, Y. Ogura, T. Ooka, K. Oshima, A. Tamura, M. Hattori, T. Hayashi posted to amplification duplication gene genome orientia sequence by treangen on 2008-11-26 11:04:57 as
	Automatic extraction of reliable regions from multiple sequence alignments [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 5. (2007) by Timo Lassmann, Erik Sonnhammer posted to 2007 accuracy alignment multiple reliability sequence by treangen on 2008-11-25 15:49:47 as along with 1 person druvus
	How Well Does the HoT Score Reflect Sequence Alignment Accuracy? [My Copy] Mol Biol Evol, Vol. 25, No. 8. (1 August 2008), pp. 1576-1580. by Barry G. Hall posted to 2008 accuracy alignment hot jctalk multiple sequence testing by treangen on 2008-11-25 15:47:13 as along with 6 people and 1 group druvus nuin gjuggler bpcusack stajich cabbagesofdoom Mycology
	Automatic assessment of alignment quality [My Copy] Nucleic Acids Research, Vol. 33, No. 22. (2005), pp. 7120-7128. by Timo Lassmann, Erik L. Sonnhammer posted to 2005 accuracy alignment quality sequence testing by treangen on 2008-11-25 15:24:50 as along with 2 people and 2 groups BioNica marcius BioinfoCIPF SGU-CIPF
	A new sequence distance measure for phylogenetic tree construction [My Copy] Bioinformatics, Vol. 19, No. 16. (1 November 2003), pp. 2122-2130. by Hasan H. Otu, Khalid Sayood posted to alignment-free distance phylogenetic sequence tree by treangen on 2008-11-25 13:00:33 as along with 1 person operon
	Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. [My Copy] Genome Biol, Vol. 6, No. 3. (2005) by S. L. Salzberg, J. C. Hotopp, A. L. Delcher, et al.M. Pop, D. R. Smith, M. B. Eisen, W. C. Nelson posted to drosophila genome sequence wolbachia by treangen on 2008-11-25 12:59:35 as along with 4 people and 2 groups operon orzenil azazello wenhan LabDros MBLAB
	The accuracy of several multiple sequence alignment programs for proteins [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (24 October 2006), 471. by Paulo Nuin, Zhouzhi Wang, Elisabeth Tillier posted to 2006 accuracy alignment multiple protein sequence by treangen on 2008-11-25 12:49:41 as along with 11 people torfinnnome natstreet BioNica daforerog druvus winterschlaefer viktor21614 gjuggler tny plofje rabio
	Evolutionary distance estimation and fidelity of pair wise sequence alignment. [My Copy] BMC bioinformatics, Vol. 6 (2005) by M. S. Rosenberg posted to 2005 accuracy alignment distance evolutionary pairwise sequence by treangen on 2008-11-25 12:47:21 as
	Stability of Multiple Alignments and Phylogenetic Trees: An Analysis of ABC-Transporter Proteins [My Copy] Algorithms for Molecular Biology, Vol. 3 (06 November 2008), 15. by Andreas W. M. Dress, Burkhard Morgenstern, Holger Wagner posted to 2008 accuracy alignment multiple phylogenetic sequence testing trees by treangen on 2008-11-25 11:42:17 as along with 2 people nuin druvus
	Noisy: identification of problematic columns in multiple sequence alignments [My Copy] Algorithms for Molecular Biology, Vol. 3 (24 June 2008), 7. by Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, et al.Stefan Grunewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler posted to 2008 accuracy alignment multiple sequence software by treangen on 2008-11-25 11:41:02 as along with 2 people druvus gjuggler
	DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. [My Copy] Algorithms for molecular biology : AMB, Vol. 3, No. 1. (27 May 2008), 6. by Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern posted to alignment dialign greedy multiple progressive segment-based sequence software by treangen on 2008-11-25 11:40:24 as along with 7 people Copper_Calcio walshtp BioNica druvus operon reyez dquest
	Ancestral sequence alignment under optimal conditions. [My Copy] BMC bioinformatics, Vol. 6 (2005) by A. K. Hudek, D. G. Brown posted to 2005 accuracy alignment gap-open multiple sequence by treangen on 2008-11-25 10:02:45 as along with 1 person druvus
	Simultaneous statistical multiple alignment and phylogeny reconstruction. [My Copy] Syst Biol, Vol. 54, No. 4. (August 2005), pp. 548-561. by R. Fleissner, D. Metzler, A. von Haeseler posted to multiple phylogeny sequence statistical-alignment by treangen on 2008-11-25 10:01:29 as along with 3 people carlk druvus AaronDarling
	Detecting Repeat Families in Incompletely Sequenced Genomes [My Copy] Algorithms in Bioinformatics (2008), pp. 342-353. by Amgarten, Jens Stoye posted to detection families genome incomplete repeat sequence wabi08 by treangen on 2008-11-25 09:58:18 as along with 2 people natstreet druvus
	Computational reconstruction of ancestral DNA sequences. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 422 (2008), pp. 171-184. by M. Blanchette, A. B. Diallo, E. D. Green, W. Miller, D. Haussler posted to 2008 accuracy alignmnent ancestral multiple phylogenetic sequence species tree by treangen on 2008-11-25 09:26:55 as along with 1 person druvus
	Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis [My Copy] Brief Bioinform (29 October 2008), bbn045. by Mohamed R. Aniba, Sophie Siguenza, Anne Friedrich, et al.Frederic Plewniak, Olivier Poch, Aron Marchler-Bauer, Julie D. Thompson posted to alignment case-study expert-systems multiple sequence by treangen on 2008-11-25 09:15:34 as along with 3 people guhjy nuin druvus
	Logarithmic gap costs decrease alignment accuracy [My Copy] BMC Bioinformatics, Vol. 7 (05 December 2006), 527. by Reed A. Cartwright posted to 2006 accuracy alignment gap gap-penalty sequence by treangen on 2008-11-24 17:42:31 as along with 4 people and 1 group timflutre druvus dpollard groepl EisenLab
	GENOMICS: Lining Up to Avoid Bias [My Copy] Science, Vol. 319, No. 5862. (25 January 2008), pp. 416-417. by Antonis Rokas posted to 2008 accuracy alignment genomics sequence testing by treangen on 2008-11-24 15:17:22 as along with 8 people operon dayjm cjeans lilou dandaman renatomilani bpcusack gjuggler
	On the significance of sequence alignments when using multiple scoring matrices. [My Copy] Bioinformatics, Vol. 20, No. 6. (12 April 2004), pp. 881-887. by F. Frommlet, A. Futschik, M. Bogdan posted to alignment evalue matrix pvalue scoring sequence significance by treangen on 2008-11-24 09:52:47 as along with 1 person and 1 group kaspermunch Bioinformatics
	SQUINT: A Multiple Alignment Program and Editor. [My Copy] Bioinformatics (7 May 2007) by Matthew G G. Goode, Allen G G. Rodrigo posted to alignment editor multiple sequence software by treangen on 2008-11-24 09:49:44 as along with 2 people Bevan_Weir grahamc
	Multiple alignment of protein sequences with repeats and rearrangements [My Copy] Nucleic Acids Research, Vol. 34, No. 20. (November 2006), pp. 5932-5942. by Phuong, Tu Minh, Do, et al.B. Chuong, Edgar, C. Robert, Batzoglou, Serafim posted to alignment multiple protein rearrangements repeats sequence software by treangen on 2008-11-24 09:47:19 as along with 2 people yylin hpaces
	Model-based prediction of sequence alignment quality [My Copy] Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2165-2171. by Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka posted to 2008 accuracy alignment multiple quality sequence sp statistical by treangen on 2008-11-24 09:45:34 as along with 3 people druvus nuin marck
	Probalign: multiple sequence alignment using partition function posterior probabilities [My Copy] Bioinformatics, Vol. 22, No. 22. (15 November 2006), pp. 2715-2721. by Roshan, Usman, Livesay, R. Dennis posted to aligment multiple posterior probabilities sequence by treangen on 2008-11-24 09:43:05 as along with 2 people druvus dakelley
	A statistical score for assessing the quality of multiple sequence alignments. [My Copy] BMC bioinformatics, Vol. 7 (03 November 2006), 484. by V. Ahola, T. Aittokallio, M. Vihinen, E. Uusipaikka posted to alignment multiple quality score sequence statistical by treangen on 2008-11-24 09:41:32 as along with 3 people nuin BioNica druvus
	Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments [My Copy] Syst Biol, Vol. 56, No. 4. (1 August 2007), pp. 564-577. by Gerard Talavera, Jose Castresana posted to 2007 accuracy alignment phylogeny protein sequence testing by treangen on 2008-11-23 01:10:53 as along with 4 people ramonvidal operon druvus Patola
	Local reliability measures from sets of co-optimal multiple sequence alignments. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2008), pp. 15-24. by G. Landan, D. Graur posted to 2008 accuracy alignment multiple reliability sequence testing by treangen on 2008-11-23 01:05:03 as
	A novel approach to local reliability of sequence alignments [My Copy] Bioinformatics, Vol. 18, No. 6. (1 June 2002), pp. 847-854. by Maximilian Schlosshauer, Mattias Ohlsson posted to 2002 accuracy alignment protein sequence testing by treangen on 2008-11-23 01:04:13 as along with 1 person rabio
	Statistical significance in biological sequence analysis. [My Copy] Brief Bioinform, Vol. 7, No. 1. (March 2006), pp. 2-24. by A. Y. Mitrophanov, M. Borodovsky posted to analysis review sequence significance statistical by treangen on 2008-11-23 01:02:10 as along with 4 people druvus Ayest xili03 wenhan
	Assessing the Discordance of Multiple Sequence Alignments [My Copy] IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 99, No. 1. (5555) by Amol Prakash, Martin Tompa posted to 2007 accuracy alignment multiple sequence statistics by treangen on 2008-11-22 22:12:23 as
	Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons [My Copy] Trends in Genetics, Vol. 22, No. 4. (April 2006), pp. 187-193. by Elliott H. Margulies, Christina W. Chen, Eric D. Green posted to 2006 accuracy alignment multiple pairwise review sequence by treangen on 2008-11-22 21:44:02 as along with 5 people and 2 groups aprasad shirleym dchughes smount gjuggler G4ID Genetics-of-Gambling
	Measuring the accuracy of genome-size multiple alignments [My Copy] Genome Biology, Vol. 8 (26 June 2007), R124. by Amol Prakash, Martin Tompa posted to 2007 accuracy alignment genome jctalk2 multiple sequence by treangen on 2008-11-22 21:41:44 as along with 5 people and 2 groups druvus dpollard AaronDarling stajich lilou EisenLab Mycology
	A probabilistic measure for alignment-free sequence comparison. [My Copy] Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3455-3461. by T. D. Pham, J. Zuegg posted to alignment-free comparison sequence by treangen on 2008-11-22 21:26:36 as along with 1 person dario
	Alignment-free sequence comparison-a review. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 4. (1 March 2003), pp. 513-523. by Susana Vinga, Jonas Almeida posted to alignment-free comparison review sequence by treangen on 2008-11-22 21:25:30 as along with 4 people mox timflutre druvus dario
	An improved string composition method for sequence comparison [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 6. (2008), S15. by Guoqing Lu, Shunpu Zhang, Xiang Fang posted to alignment alignment-free comparison composition multiple sequence string by treangen on 2008-11-22 21:17:16 as along with 1 person druvus
	An overview of multiple sequence alignment. [My Copy] Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], Vol. Chapter 3 (November 2003) by V. Simossis, J. Kleinjung, J. Heringa posted to alignment multiple review sequence by treangen on 2008-11-22 21:14:39 as
	Multiple sequence alignment. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 143-161. by W. Pirovano, J. Heringa posted to alignment multiple review sequence by treangen on 2008-11-22 21:10:10 as along with 1 person druvus
	Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments. [My Copy] Mol Biol Evol (20 August 2007) by Tanya Golubchik, Michael J J. Wise, Simon Easteal, Lars S S. Jermiin posted to 2007 accuracy alignment gaps jctalk multiple sequence testing by treangen on 2008-11-22 21:01:53 as along with 7 people natstreet BioNica druvus zwang lilou dandaman caseybrown
	Learning scoring schemes for sequence alignment from partial examples. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 5, No. 4. (c 2008), pp. 546-556. by E. Kim, J. Kececioglu posted to 2008 accuracy alignment parameters parametric scoring sequence by treangen on 2008-11-22 20:47:53 as along with 1 person darian
	A probabilistic model of local sequence alignment that simplifies statistical significance estimation. [My Copy] PLoS computational biology, Vol. 4, No. 5. (30 May 2008), e1000069. by Sean R. Eddy posted to alignment local model sequence statistics by treangen on 2008-11-22 17:27:04 as along with 9 people cmzmasek druvus vwchan BioNica saerni dakelley aramesh2 Ema gdb
	Measuring Global Credibility with Application to Local Sequence Alignment [My Copy] PLoS Comput Biol, Vol. 4, No. 5. (16 May 2008), e1000077. by Bobbie-Jo M. Webb-Robertson, Lee A. Mccue, Charles E. Lawrence posted to 2008 accuracy alignment local sequence testing by treangen on 2008-11-22 14:44:45 as along with 4 people sconlan mhamada mariakmejia gdb
	Multiple sequence alignment accuracy and evolutionary distance estimation. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by M. S. Rosenberg posted to 2005 accuracy alignment alignment-accuracy multiple sequence by treangen on 2008-11-21 19:26:55 as along with 3 people and 2 groups aprasad dpollard cisevol EisenLab cis-regulatory-evolution
	Finding functional sequence elements by multiple local alignment [My Copy] Nucl. Acids Res., Vol. 32, No. 1. (2 January 2004), pp. 189-200. by Martin C. Frith, Ulla Hansen, John L. Spouge, Zhiping Weng posted to alignment local multiple sequence by treangen on 2008-11-21 19:23:28 as along with 6 people and 1 group wyatt111 idonaldson wowalz dquest kengg nklee Plantandetc
	Local multiple sequence alignment using dead-end elimination [My Copy] Bioinformatics, Vol. 15, No. 11. (1 November 1999), pp. 947-953. by Lukashin, Rosa posted to alignment lma local multiple sequence by treangen on 2008-11-21 14:37:53 as

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alignment	96
genome	96
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