aprasad's alignment [40 articles] Export

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

	BLAT--the BLAST-like alignment tool. [My Copy] Genome research, Vol. 12, No. 4. (1 April 2002), pp. 656-664. by James J. Kent posted to tools software alignment by aprasad on 2009-09-30 21:52:48 as along with 37 people and 3 groups azazello rshe dchughes rdowell gwallau druvus maria_hauser n00c sficklin Thaverkamp cpwardell daveGerrard coela daforerog pwais umit mmartin paszkows operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre olympos cjeans wenhan natstreet antonkratz yoanjacquemin talponer bozdagd gpappas LabDros BergmanLab EisenLab
	Aligning multiple genomic sequences with the threaded blockset aligner. [My Copy] Genome research, Vol. 14, No. 4. (April 2004), pp. 708-715. by Mathieu Blanchette, James J. Kent, Cathy Riemer, et al.Laura Elnitski, Arian F. Smit, Krishna M. Roskin, Robert Baertsch, Kate Rosenbloom, Hiram Clawson, Eric D. Green, David Haussler, Webb Miller posted to tba msa alignment by aprasad on 2009-08-19 23:27:51 as along with 13 people and 1 group roys emptyhb nuin APRegier operon ujh indigoviolet csardas djkt yylin Neeperando maralena AlexanderPico EisenLab
	trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1972-1973. by Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón posted to alignment alignment_error methods phylogenetics tools by aprasad on 2009-08-10 15:09:34 as along with 3 people and 1 group gjuggler ollieredfernwork nuin Orengo Group Journal Picks
	Multiple Sequence Alignment in Phylogenetic Analysis [My Copy] Molecular Phylogenetics and Evolution, Vol. 16, No. 3. (September 2000), pp. 317-330. by A. Phillips, D. Janies, W. Wheeler posted to alignment methods phylogenetics simultaneous_inference by aprasad on 2009-06-24 22:10:41 as along with 4 people operon nuin ziquje stormybriggs
	Simultaneous phylogeny reconstruction and multiple sequence alignment [My Copy] BMC Bioinformatics, Vol. 10, No. Suppl 1. (2009), S11. by Feng Yue, Jian Shi, Jijun Tang posted to alignment phylogenetics simultaneous_inference tools by aprasad on 2009-06-24 22:07:55 as along with 1 person cmzmasek
	Fast Statistical Alignment [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (29 May 2009), e1000392. by Robert K. Bradley, Adam Roberts, Michael Smoot, et al.Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, Lior Pachter posted to alignment methods tools by aprasad on 2009-06-24 16:25:39 as along with 18 people and 1 group seb1 rdowell timflutre natstreet n00c yylin Gorzomagnificent guhjy dakelley reyez rec3141 farhat operon bmduggan nuin AlexBateman djkt druvus Journal picks
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, Randal C. Linder, Tandy Warnow posted to alignment joint methods phylogenetics tools by aprasad on 2009-06-22 21:56:14 as along with 26 people and 4 groups gjuggler parnell kinestetika robertrentzsch xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky timflutre inquil TRHvidsten djkt fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks iSEEM
	The Jalview Java alignment editor. [My Copy] Bioinformatics, Vol. 20, No. 3. (12 February 2004), pp. 426-427. by M. Clamp, J. Cuff, S. M. Searle, G. J. Barton posted to alignment jalview tools by aprasad on 2009-03-05 22:08:15 as along with 3 people and 2 groups jwm CharlesM kcrawlik Radiation_Damage Stressosome
	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 alignment alignment_error msa by aprasad on 2009-03-05 21:26:45 as along with 5 people and 2 groups treangen shirleym dchughes smount gjuggler G4ID Genetics-of-Gambling
	Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (16 March 2006) by Rahul Siddharthan posted to alignment msa non-coding tools by aprasad on 2009-01-06 20:06:33 as along with 3 people and 2 groups cisevol dpollard lilou cis-regulatory-evolution EisenLab
	Tools for simulating evolution of aligned genomic regions with integrated parameter estimation [My Copy] Genome Biology, Vol. 9, No. 10. (08 October 2008), R147. by Avinash Varadarajan, Robert K. Bradley, Ian H. Holmes posted to alignment evolution sequence simulation tools by aprasad on 2008-10-14 17:51:48 as along with 9 people inquil mhamada markusd nuin djkt treangen gjuggler pengchy druvus
	Segment-based multiple sequence alignment [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192. by Tobias Rausch, Anne K. Emde, David Weese, Andreas Doring, Cedric Notredame, Knut Reinert posted to alignment methods msa tools by aprasad on 2008-08-13 18:59:33 as along with 9 people nuin BioNica darian Md_2007 zwang Ema APRegier djkt groepl
	NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences. [My Copy] Genomics (27 May 2008) by Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. F. Stadler, Jörg Hackermüller posted to alignment methods msa tools by aprasad on 2008-07-30 16:16:50 as along with 1 person maximilianh
	Characterization of pairwise and multiple sequence alignment errors. [My Copy] Gene (3 June 2008) by Giddy Landan, Dan Graur posted to alignment alignment_error phylogenetic_accuracy simulation by aprasad on 2008-07-14 15:48:01 as
	Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis [My Copy] Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635. by Ari Loytynoja, Nick Goldman posted to alignment indel methods by aprasad on 2008-06-23 19:05:48 as along with 29 people and 3 groups memerman operon TRHvidsten BioNica cmzmasek timflutre pradiptaray alexeid marti bpcusack hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
	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 alignment est indel phylogenetics phylogenomics by aprasad on 2008-05-09 17:56:28 as along with 7 people and 2 groups sriesenfeld skembel treangen natstreet druvus stajich Patola iSEEM Mycology
	Computation and Analysis of Genomic Multi-Sequence Alignments [My Copy] Annual Review of Genomics and Human Genetics, Vol. 8, No. 1. (9 May 2007), pp. 193-213. by Mathieu Blanchette posted to alignment methods review by aprasad on 2008-05-06 19:35:12 as along with 7 people and 1 group natstreet druvus treangen dpollard lilou nklee maximilianh EisenLab
	Analysis of chimpanzee history based on genome sequence alignments. [My Copy] PLoS genetics, Vol. 4, No. 4. (April 2008) by J. L. Caswell, S. Mallick, D. J. Richter, et al.J. Neubauer, C. Schirmer, S. Gnerre, D. Reich posted to alignment chimp human lineage_sorting tree by aprasad on 2008-04-25 20:24:29 as along with 2 people madreach reyez
	Uncertainty in homology inferences: assessing and improving genomic sequence alignment. [My Copy] Genome research, Vol. 18, No. 2. (1 February 2008), pp. 298-309. by Gerton Lunter, Andrea Rocco, Naila Mimouni, Andreas Heger, Alexandre Caldeira, Jotun Hein posted to alignment methods tools by aprasad on 2008-02-07 18:56:32 as along with 8 people brant treangen djkt grahamc dandaman mailund gjuggler AaronDarling
	Alignment Uncertainty and Genomic Analysis [My Copy] Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476. by Karen M. Wong, Marc A. Suchard, John P. Huelsenbeck posted to alignment genomics methods phylogenetics by aprasad on 2008-01-26 18:15:23 as along with 33 people and 2 groups Jporci operon walshtp darian ptrobajo friendpine skembel druvus treangen bpb dayjm pradiptaray dpollard tny djkt cjeans zwang lisa1 cactus biomcgary lilou dandaman gjuggler renatomilani mclarenv youdon bpcusack guhjy jdelcampo adacier gracio timflutre jfr EisenLab microbiology_nijmegen
	28-Way vertebrate alignment and conservation track in the UCSC Genome Browser [My Copy] Genome Res. (5 November 2007), gr.6761107. by Webb Miller, Kate Rosenbloom, Ross C. Hardison, et al.Minmei Hou, James Taylor, Brian Raney, Richard Burhans, David C. King, Robert Baertsch, Daniel Blankenberg, Kosakovsky, Anton Nekrutenko, Belinda Giardine, Robert S. Harris, Svitlana Tyekucheva, Mark Diekhans, Thomas H. Pringle, William J. Murphy, Arthur Lesk, George M. Weinstock, Kerstin L. Toh, Richard A. Gibbs, Eric S. Lander, Adam Siepel, David Haussler, James W. Kent posted to alignment comparative_genomics ucsc by aprasad on 2007-12-11 14:46:01 as along with 11 people rschulz dchughes nklee maximilianh idonaldson fpattyn gjuggler clearbluespring joavah AaronDarling guhjy
	Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment [My Copy] Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 289-297. by Jaebum Kim, Saurabh Sinha posted to alignment indel tools by aprasad on 2007-09-02 13:38:06 as along with 4 people and 1 group timflutre gjuggler druvus indigoviolet EisenLab
	Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments [My Copy] Mol Biol Evol, Vol. 24, No. 6. (1 June 2007), pp. 1380-1383. by Giddy Landan, Dan Graur posted to alignment methods by aprasad on 2007-08-09 21:11:14 as along with 9 people and 1 group treangen druvus rvosa BioNica stajich cjeans zwang lilou mailund FAB-lab
	PipMaker---A Web Server for Aligning Two Genomic DNA Sequences [My Copy] Genome Res., Vol. 10, No. 4. (1 April 2000), pp. 577-586. by Scott Schwartz, Zheng Zhang, Kelly A. Frazer, et al.Arian Smit, Cathy Riemer, John Bouck, Richard Gibbs, Ross Hardison, Webb Miller posted to alignment pipmaker tools by aprasad on 2007-07-31 16:20:58 as along with 4 people Neeperando michC adijr wenhan
	Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments [My Copy] BMC Bioinformatics, Vol. 7 (14 August 2006), 376. by Daniel A. Pollard, Alan M. Moses, Venky N. Iyer, Michael B. Eisen posted to alignment msa regulatory tba tools by aprasad on 2007-07-13 23:11:25 as along with 6 people and 2 groups dpollard lusk Garamonfok lilou cisevol emptyhb EisenLab cis-regulatory-evolution
	Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. [My Copy] Nucleic Acids Res (8 May 2007) by Jake, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander posted to alignment phylogenetics phylogenomics tools by aprasad on 2007-05-14 01:43:21 as
	Incorporating indel information into phylogeny estimation for rapidly emerging pathogens [My Copy] BMC Evolutionary Biology, Vol. 7, No. 1. (14 March 2007), 40. by Benjamin D. Redelings, Marc A. Suchard posted to alignment bayesian indel methods phylogenetics by aprasad on 2007-05-14 01:38:56 as along with 5 people and 1 group timflutre druvus operon dpollard stajich EisenLab
	Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. [My Copy] Molecular biology and evolution, Vol. 17, No. 4. (1 April 2000), pp. 540-552. by J. Castresana posted to alignment conservation gblocks phylogenetics tools by aprasad on 2007-04-18 15:35:13 as along with 9 people and 1 group biomcgary ramonvidal operon druvus dmp treangen stajich ArtemPankin cmzmasek Mycology
	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 alignment ortholog phylogenetics phylogenomics tools by aprasad on 2007-02-12 19:30:28 as along with 7 people calderonv treangen natstreet druvus operon akifumi dmp
	Multiple sequence alignment: In pursuit of homologous DNA positions [My Copy] Genome Res., Vol. 17, No. 2. (1 February 2007), pp. 127-135. by Sudhir Kumar, Alan Filipski posted to msa methods alignment by aprasad on 2007-02-08 16:00:23 as along with 8 people and 1 group Thaverkamp natstreet druvus treangen indigoviolet BioNica cjeans mingzhi EisenLab
	Assessment of phylogenomic and orthology approaches for phylogenetic inference. [My Copy] Bioinformatics (19 January 2007) by B. E. E. Dutilh, V. van Noort, van der Heijden, T. Boekhout, B. Snel, M. A. A. Huynen posted to whole_genome phylogenomics phylogenetics ortholog alignment by aprasad on 2007-01-29 14:41:46 as along with 1 person inquil
	MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3518-3524. by Scott Schwartz, Laura Elnitski, Mei Li, et al.Matt Weirauch, Cathy Riemer, Arian Smit, Nisc C. Program, Eric D. Green, Ross C. Hardison, Webb Miller posted to algorithm alignment horse pipmaker tools by aprasad on 2006-09-04 20:27:15 as along with 4 people danatcaret stharward druvus wenhan
	CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. [My Copy] Nucleic acids research, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680. by J. D. Thompson, D. G. Higgins, T. J. Gibson posted to alignment phylogenetics tools by aprasad on 2006-08-25 14:57:28 as along with 34 people and 1 group biomcgary vprieto tomjad oceanwind Blackbeard db344 udivi daforerog Md_2007 sebk cen4ik usagi-kirin jmw greger_halltorp jshapiro mercaptan evaf caldavis miguel onlyrey bjorns RMGraze moborg arcticrasta dullhunk caporaso ahanora Haggan BioNica timflutre adijr xingxu newton1234 Lombardo_7 biomedical-nlp
	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 alignment long_branch_attraction msa phylogenetics simulation by aprasad on 2006-08-25 14:41:21 as along with 4 people gjuggler druvus treangen akifumi
	BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. [My Copy] Bioinformatics (5 May 2006) by Marc A. A. Suchard, Benjamin D. D. Redelings posted to alignment phylogenetics tools by aprasad on 2006-08-25 14:37:02 as along with 6 people and 1 group vivianm treangen alexeid eckart_bindewald indigoviolet AaronDarling EisenLab
	Combining phylogenetic and hidden Markov models in biosequence analysis. [My Copy] J Comput Biol, Vol. 11, No. 2-3. (2004), pp. 413-428. by A. Siepel, D. Haussler posted to algorithm alignment phylogenetics by aprasad on 2006-08-25 14:36:06 as along with 4 people and 1 group mgledi rschulz timflutre bioinfo KCL & UCL Bioinformatics
	SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by A. C. Shih, D. T. Lee, L. Lin, et al.C. L. Peng, S. H. Chen, Y. W. Wu, C. Y. Wong, M. Y. Chou, T. C. Shiao, M. F. Hsieh posted to alignment methods tools by aprasad on 2006-05-09 13:42:33 as along with 2 people lilou chodar
	Multiple sequence alignment accuracy and evolutionary distance estimation. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by M. S. Rosenberg posted to alignment comparative_genomics evolution by aprasad on 2006-04-10 19:16:26 as along with 3 people and 2 groups treangen dpollard cisevol EisenLab cis-regulatory-evolution
	Genomic multiple sequence alignments: refinement using a genetic algorithm. [My Copy] BMC Bioinformatics, Vol. 6 (8 August 2005) by C. Wang, E. J. Lefkowitz posted to alignment genomic msa by aprasad on 2005-10-03 20:22:46 as
	ABC: software for interactive browsing of genomic multiple sequence alignment data. [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (8 December 2004) by G. M. Cooper, S. A. Singaravelu, A. Sidow posted to alignment analysis evolution genomic msa tools by aprasad on 2005-08-22 15:27:51 as along with 1 person Garamonfok

Note: You may cite this page as: http://www.citeulike.org/user/aprasad/tag/alignment

phylogenetics	249
tree	119
evolution	109
methods	107
genome_size	88
review	71
mammal	71
tools	70
genome_evolution	54
indel	51
repeats	47
mutation_rate	45
comparative_genomics	44
phylogenomics	44
bat	43
selection	41
alignment	40
regulatory	39
genome	37
congruence	35
bayesian	33
whole_genome	32
cns	31
transposon	29
human_genome	26
genomics	26
primate	25
likelihood	24
coding	22
population_genetics	21
human	19
mutation	18
gc	17
sequence	17
rare_genomic_characters	17
retrotransposon	16
algorithm	16
substitution_rate	16
simulation	15
platyrrhini	13
element	12
model	12
congruence_landscapes	12
mitochondria	11
root_eutheria	11
time	11
conservation	11
mcs	10
nisc	10
jc	10
homo-pan-gorilla	10
chimp	10
msa	10
bacteria	10
isochore	10
parsimony	10
lineage_sorting	9
morphology	9
functional	9
plants	9
motif	9
tfbs	9
bac	9
theria	9
encode	8
recombination	8
long_branch_attraction	8
speciation	8
non-coding	8
flying_dna	8
horizontal_gene_transfer	8
phil	8
mouse	7
tree_visualization	7
signature	6
repeat	6
model_choice	6
phylogenetic_accuracy	6
nucleotypic_effect	6
time_tree	6
indel_rate	6
molecular_clock	6
sox10	6
consensus	6
coalescent	6
book	6
drosophila	6
rodents	6
missing_data	6
monotreme	5
cpg	5
gdf6	5
variation	5
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bird	5
fish	5
ultraconserved	5
gene_geneology	5
colorectal_cancer	5
enhancer	5
chicken	5
theory	5
glires	5
molecular_evolution	5
hmm	5
map	5
ortholog	5
plant	5
ncrna	5
binfo	5
rearrangement	5
methylation	5
yeast	5
promoter	5
protein	4
ild	4
bac_mapping	4
neutral	4
model_selection	4
placental	4
star_paradox	4
exon	4
murphy	4
correlations	4
chromatin	4
joint	4
zooseq	4
ucsc	4
ry_coding	4
genomic	4
analysis	4
atlantogenata	4
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splicing	4
afrotheria	4
intrinsic_features	4
alignment_error	4
supertree	4
overgo	4
signal	4
chip	4
genome_paper	4
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exactplus	3
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root	3
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skin	3
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island	3
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dog	3
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est	2
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systematic	1
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genetic_disease	1
hplc	1
biofuel	1
fossil	1
replication	1
perissodactylas	1
dcodeorg	1
gencode	1
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cow	1
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nature	1
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nj	1
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wgs	1
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nylon	1
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cat	1
coyote	1
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trees	1
me	1
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r	1
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usage	1
molecular_biology	1
melan-a	1
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uprobe	1
history-of-science	1
shark	1
fugu	1
chip-chip	1
fly	1
darwin	1
euarchontoglires	1
opossum	1
physical	1

aprasad's alignment [40 articles] Export

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