treangen's alignment [96 articles] Export

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

	The meaning of alignment: lessons from structural diversity [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Walter Pirovano, Anton K. Feenstra, Jaap Heringa posted to alignment protein structure by treangen on 2009-01-07 10:56:30 as along with 13 people pimmy swtimmer dimka mhamada reyez markusd j3xucite nuin kshameer druvus chad_davis taguchi pansapiens
	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
	Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? [My Copy] BMC Evolutionary Biology, Vol. 8 (26 March 2008), 95. by Stefanie Hartmann, Todd J. Vision posted to 2008 accuracy alignment gap by treangen on 2008-12-08 13:57:44 as along with 7 people and 2 groups sriesenfeld skembel natstreet druvus stajich Patola aprasad iSEEM Mycology
	Multiple Sequence Alignment Accuracy and Phylogenetic Inference [My Copy] Systematic Biology, Vol. 55, No. 2. (April 2006), pp. 314-328. by T. Ogdenw, Michael Rosenberg posted to 2006 accuracy alignment jctalk by treangen on 2008-12-08 13:30:34 as along with 3 people druvus aprasad akifumi
	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
	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
	Multiple genome alignment for identifying the core structure among moderately related microbial genomes [My Copy] BMC Genomics, Vol. 9 (31 October 2008), 515. by Ikuo Uchiyama posted to alignment bacteria core corealigner genome multiple software by treangen on 2008-11-25 10:12:48 as along with 2 people azazello druvus
	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
	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
	StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. [My Copy] Bioinformatics (Oxford, England) (27 August 2008) by Adám Novák, István Miklós, Rune Lyngsø, Jotun Hein posted to alignment bayesian software statistical-alignment by treangen on 2008-11-24 17:56:52 as along with 4 people and 1 group vivianm stajich druvus nuin Mycology
	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
	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
	Robust E-values for gapped local alignments. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 13, No. 4. (May 2006), pp. 882-896. by D. Metzler posted to alignment evalue gapped local poisson review by treangen on 2008-11-23 01:03:34 as along with 1 person druvus
	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
	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
	Sequence alignment with an appropriate substitution matrix. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 2. (March 2008), pp. 129-138. by X. Huang posted to alignment gap-penalty local matrix parameters substitution by treangen on 2008-11-22 20:49:18 as
	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
	Assessing the Accuracy of Ancestral Protein Reconstruction Methods [My Copy] PLoS Comput Biol, Vol. 2, No. 6. (23 June 2006), e69. by Paul D. Williams, David D. Pollock, Benjamin P. Blackburne, Richard A. Goldstein posted to 2006 accuracy alignment evolution phylogeny protein by treangen on 2008-11-22 17:34:01 as along with 2 people cmzmasek cjeans
	Parametric Alignment of Drosophila Genomes [My Copy] PLoS Computational Biology, Vol. 2, No. 6. (1 June 2006), e73. by Colin N. Dewey, Peter M. Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter posted to alignment genome parameters parametric phmm by treangen on 2008-11-22 17:32:47 as along with 3 people and 1 group emilyhare dquest joshuashen EisenLab
	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
	Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. [My Copy] Science (New York, N.Y.), Vol. 262, No. 5131. (8 October 1993), pp. 208-214. by C. E. Lawrence, S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, J. C. Wootton posted to alignment gibbs local multiple by treangen on 2008-11-21 14:39:56 as along with 10 people isimpson rsaito Mehlhorn dquest AaronDarling johncumbers jguinney xili03 seitentaisei wenhan
	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
	State of the art: refinement of multiple sequence alignments [My Copy] BMC Bioinformatics, Vol. 7 (14 November 2006), 499. by Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant posted to 2006 accuracy alignment multiple refinement sequence by treangen on 2008-11-21 13:40:44 as along with 2 people natstreet druvus
	Dynamic programming alignment accuracy [My Copy] In RECOMB '98: Proceedings of the second annual international conference on Computational molecular biology (1998), pp. 102-108. by Ian Holmes, Richard Durbin posted to 1998 accuracy alignment dynamic programming by treangen on 2008-11-21 13:37:21 as along with 1 person yylin
	Clustal W and Clustal X version 2.0 [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2947-2948. by M. A. Larkin, G. Blackshields, N. P. Brown, et al.R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, D. G. Higgins posted to alignment clustal multiple sequence software by treangen on 2008-11-21 13:22:46 as along with 18 people l00cas vprieto Copper_Calcio TLVincent tomjad BioNica udivi Keksle hpm druvus jwm cassj lisa1 ryanraaum bmaust alanrw mschofie marck

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alignment	96
genome	96
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treangen's alignment [96 articles] Export

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