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aprasads alignment [30 articles]

Neue Publikationen in aprasads Bibliothek eingetragen unter dem Bezeichner: alignment. You can also see everyone's alignment.
  • Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
    Genome Biology, Vol. 9 (08 October 2008), R147.
    by Avinash Varadarajan, Robert K Bradley, Ian H Holmes
    posted to tools simulation sequence evolution alignment by aprasad on 2008-10-14 17:51:48 as ** along with 5 people djkt treangen gjuggler pengchy druvus
  • Segment-based multiple sequence alignment
    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 6 people Md_2007 zwang Ema APRegier djkt groepl
  • NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences.
    Genomics (27 May 2008)
    by Dominic Rose, Jana Hertel, Kristin Reiche, Peter FF 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.
    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
    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 23 people and 3 groups 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?
    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 4 people and 1 group natstreet druvus stajich Patola Berkeley Mycology
  • Computation and Analysis of Genomis Multi-Sequence Alignments.
    Annu Rev Genomics Hum Genet (9 May 2007)
    by Mathieu Blanchette
    posted to alignment methods review by aprasad on 2008-05-06 19:35:12 as ** along with 5 people and 1 group treangen dpollard lilou nklee maximilianh EisenLab
  • Analysis of chimpanzee history based on genome sequence alignments.
    PLoS genetics, Vol. 4, No. 4. (April 2008)
    by JL Caswell, S Mallick, DJ Richter, 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
    Genome Res., 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
    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 27 people and 2 groups druvus treangen bpb dayjm pradiptaray dpollard tny djkt cjeans zwang lisa1 cactus biomcgary lilou kinestetika 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
    Genome Res. (5 November 2007), gr.6761107.
    by Webb Miller, Kate Rosenbloom, Ross C Hardison, 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 10 people dchughes nklee maximilianh idonaldson fpattyn gjuggler clearbluespring joavah AaronDarling guhjy
  • Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
    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
    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
    Genome Res., Vol. 10, No. 4. (1 April 2000), pp. 577-586.
    by Scott Schwartz, Zheng Zhang, Kelly A Frazer, 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 3 people michC adijr wenhan
  • Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    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.
    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
    BMC Evolutionary Biology, Vol. 7 (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 4 people and 1 group druvus operon dpollard stajich EisenLab
  • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
    Mol Biol Evol, Vol. 17, No. 4. (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 6 people and 1 group druvus dmp treangen stajich ArtemPankin cmzmasek Berkeley Mycology
  • SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
    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 6 people treangen natstreet druvus operon akifumi dmp
  • Multiple sequence alignment: In pursuit of homologous DNA positions
    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 7 people and 1 group natstreet druvus treangen indigoviolet BioNica cjeans mingzhi EisenLab
  • Assessment of phylogenomic and orthology approaches for phylogenetic inference.
    Bioinformatics (19 January 2007)
    by BEE Dutilh, V van Noort, van der Heijden, T Boekhout, B Snel, MAA Huynen
    posted to whole_genome phylogenomics phylogenetics ortholog alignment by aprasad on 2007-01-29 14:41:46 as **
  • MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3518-3524.
    by Scott Schwartz, Laura Elnitski, Mei Li, 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 1 person wenhan
  • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680.
    by JD Thompson, DG Higgins, TJ Gibson
    posted to alignment phylogenetics tools by aprasad on 2006-08-25 14:57:28 as ** along with 28 people and 1 group 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 leelarcombe timflutre adijr xingxu newton1234 Lombardo_7 biomedical-nlp
  • Multiple Sequence Alignment Accuracy and Phylogenetic Inference
    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 1 person akifumi
  • BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.
    Bioinformatics (5 May 2006)
    by Marc AA Suchard, Benjamin DD Redelings
    posted to alignment phylogenetics tools by aprasad on 2006-08-25 14:37:02 as * along with 5 people and 1 group treangen alexeid eckart_bindewald indigoviolet AaronDarling EisenLab
  • Combining phylogenetic and hidden Markov models in biosequence analysis.
    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 1 person bioinfo
  • SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools.
    BMC Bioinformatics, Vol. 7 (2006)
    by AC Shih, DT Lee, L Lin, CL Peng, SH Chen, YW Wu, CY Wong, MY Chou, TC Shiao, MF 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.
    BMC Bioinformatics, Vol. 6 (2005)
    by MS 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.
    BMC Bioinformatics, Vol. 6 (8 August 2005)
    by C Wang, EJ 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.
    BMC Bioinformatics, Vol. 5, No. 1. (8 December 2004)
    by GM Cooper, SA 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
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