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aprasads tools [41 articles]

Neue Publikationen in aprasads Bibliothek eingetragen unter dem Bezeichner: tools. You can also see everyone's tools.
  • A Rapid Bootstrap Algorithm for the RAxML Web Servers
    Systematic Biology, Vol. 57, No. 5. (October 2008), pp. 758-771.
    by Stamatakis, Alexandros, Hoover, Paul, Rougemont, Jacques
    posted to tools raxml phylogenetics likelihood by aprasad on 2008-10-23 04:28:27 as **
  • REJECTOR: Software for Population History Inference from Genetic Data via a Rejection Algorithm
    Bioinformatics (20 October 2008), btn540.
    by Matthew J Jobin, Joanna L Mountain
    posted to tools simulation population_genetics method demography coalescent by aprasad on 2008-10-22 17:14:16 as ** along with 1 person djkt
  • 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
  • Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies
    Systematic Biology, Vol. 57, No. 5. (2008), pp. 785-794.
    by Tom M Nye
    posted to tree_visualization tree_comparison tools phylogenetics by aprasad on 2008-10-13 18:26:30 as **
  • F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags.
    Bioinformatics (Oxford, England) (10 September 2008)
    by Alan PP Boyle, Justin Guinney, Gregory EE Crawford, Terrence SS Furey
    posted to tools tag sequence bed by aprasad on 2008-09-15 02:37:16 as ** along with 3 people polivares cthachuk zhouyu
  • 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
  • jModelTest: Phylogenetic Model Averaging
    Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1253-1256.
    by David Posada
    posted to methods model_choice tools by aprasad on 2008-06-26 21:29:49 as **
  • primetv: A viewer for reconciled trees
    BMC Bioinformatics, Vol. 8 (07 May 2007), 148.
    by Bengt Sennblad, Eva Schreil, Ann, Jens Lagergren, Lars Arvestad
    posted to methods tools tree_visualization by aprasad on 2008-06-19 22:45:22 as ** along with 1 person gendlerk
  • Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences.
    Syst Biol, Vol. 56, No. 6. (December 2007), pp. 988-1010.
    by DA Morrison
    posted to likelihood methods phylogenetics tools by aprasad on 2008-03-29 08:24:22 as ** along with 2 people druvus akifumi
  • 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
  • A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
    Bioinformatics, Vol. 22, No. 1. (1 January 2006), pp. 117-119.
    by Tom M Nye, Pietro Lio, Walter R Gilks
    posted to tools tree_comparison tree_visualization by aprasad on 2008-02-06 23:19:37 as ** along with 2 people dparks blindAngle
  • Paloverde: an OpenGL 3-D phylogeny browser.
    Bioinformatics (24 February 2006)
    by Michael JJ Sanderson
    posted to phylogenetics tools tree_visualization by aprasad on 2008-02-06 22:52:01 as ** along with 3 people dparks eckart_bindewald akifumi
  • Analysis and Visualization of Tree Space
    Systematic Biology, Vol. 54, No. 3. (June 2005), pp. 471-482.
    by David Hillis, Tracy Heath, Katherine John
    posted to phylogenetics tools tree_visualization by aprasad on 2008-02-06 22:49:40 as **
  • OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics
    BMC Evolutionary Biology, Vol. 7 (30 November 2007), 241.
    by Vincent Ranwez, Frederic Delsuc, Sylvie Ranwez, Khalid Belkir, Marie K Tilak, Emmanuel JP Douzery
    posted to database mammalian phylogenetics tools by aprasad on 2008-01-25 16:10:13 as ** along with 1 person idonaldson
  • RadCon: phylogenetic tree comparison and consensus
    Bioinformatics, Vol. 16, No. 5. (1 May 2000), pp. 486-487.
    by Joseph L Thorley, Roderic D Page
    posted to consensus phylogenetics tools tree by aprasad on 2008-01-16 20:37:13 as ** along with 2 people tny sterovetta
  • Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference.
    Nat Protoc, Vol. 2, No. 11. (2007), pp. 3022-3030.
    by WJ Murphy, SJ O'Brien
    posted to comparative_genomics map methods primer tools by aprasad on 2007-11-26 15:09:24 as **
  • INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events.
    Nucleic Acids Res (21 May 2007)
    by Feng, Chueng, Trees
    posted to indel methods tools by aprasad on 2007-09-13 22:20:10 as ** along with 5 people and 1 group natstreet druvus guhjy dpollard lilou EisenLab
  • DNA assembly with gaps (Dawg): simulating sequence evolution.
    Bioinformatics, Vol. 21 Suppl 3 (1 November 2005)
    by RA Cartwright
    posted to evolution phylogenetics sequence simulation tools by aprasad on 2007-09-10 15:50:05 as ** along with 2 people timflutre gjuggler
  • 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
  • CONSEL: for assessing the confidence of phylogenetic tree selection.
    Bioinformatics, Vol. 17, No. 12. (December 2001), pp. 1246-1247.
    by H Shimodaira, M Hasegawa
    posted to consel likelihood methods tools by aprasad on 2007-08-31 21:55:04 as read along with 2 people druvus polpotak
  • 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 **
  • GRIL: genome rearrangement and inversion locator.
    Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 122-124.
    by AE Darling, B Mau, FR Blattner, NT Perna
    posted to microinversions synteny tools by aprasad on 2007-04-18 15:45:17 as ** along with 3 people operon AaronDarling treangen
  • 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
  • Developments in CORG: a gene-centric comparative genomics resource.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by C Dieterich, MW Franz, M Vingron
    posted to comparative_genomics non-coding regulatory tools by aprasad on 2007-02-12 18:01:55 as **
  • TreeQ-VISTA: An Interactive Tree Visualization Tool with Functional Annotation Query Capabilities.
    Bioinformatics (17 January 2007)
    by Shengyin Gu, Iain Anderson, Victor Kunin, Michael Cipriano, Simon Minovitsky, Gunther Weber, Nina Amenta, Bernd Hamann, Inna Dubchak
    posted to phylogenetics tools by aprasad on 2007-02-02 14:23:09 as ** along with 2 people and 1 group guhjy indigoviolet EisenLab
  • 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
  • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
    Syst Biol, Vol. 52, No. 5. (October 2003), pp. 696-704.
    by S Guindon, O Gascuel
    posted to likelihood phylogenetics phyml tools by aprasad on 2006-08-25 14:53:12 as ** along with 8 people and 1 group druvus bpb chrn lyongu treangen Haggan cdallett Auger Dead 60's
  • 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
  • Incorporating information from length-mutational events into phylogenetic analysis
    Molecular Phylogenetics and Evolution, Vol. 38, No. 3. (March 2006), pp. 667-676.
    by Kai Muller
    posted to indel phylogenetics tools by aprasad on 2006-08-25 14:32:21 as ** along with 2 people and 1 group druvus cmm FAB-lab
  • 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
  • Galaxy: a platform for interactive large-scale genome analysis.
    Genome Res, Vol. 15, No. 10. (October 2005), pp. 1451-1455.
    by B Giardine, C Riemer, RC Hardison, R Burhans, L Elnitski, P Shah, Y Zhang, D Blankenberg, I Albert, J Taylor, W Miller, WJ Kent, A Nekrutenko
    posted to comparative_genomics galaxy genome tools by aprasad on 2006-04-10 19:16:08 as ** along with 2 people daforerog guhjy
  • De novo identification of repeat families in large genomes.
    Bioinformatics, Vol. 21 Suppl 1 (1 June 2005)
    by AL Price, NC Jones, PA Pevzner
    posted to binfo repeats tools by aprasad on 2006-03-31 23:02:46 as ** along with 5 people treangen druvus hoangmit timflutre urgi
  • notes Automated de novo identification of repeat sequence families in sequenced genomes.
    Genome Res, Vol. 12, No. 8. (August 2002), pp. 1269-1276.
    by Z Bao, SR Eddy
    posted to binfo recon repeats tools by aprasad on 2006-01-02 18:02:59 as ** along with 5 people timflutre Jporci urgi yoanjacquemin Neeperando
  • The CpG island searcher: a new WWW resource.
    In Silico Biol, Vol. 3, No. 3. (2003), pp. 235-240.
    by D Takai, PA Jones
    posted to cpg human_genome island tools by aprasad on 2005-09-12 21:32:29 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
  • Dcode.org anthology of comparative genomic tools.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by GG Loots, I Ovcharenko
    posted to analysis comparative_genomics dcodeorg genomic tools web by aprasad on 2005-08-18 19:47:39 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
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