These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

249 related articles for article (PubMed ID: 21636595)

  • 1. Aligning short reads to reference alignments and trees.
    Berger SA; Stamatakis A
    Bioinformatics; 2011 Aug; 27(15):2068-75. PubMed ID: 21636595
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.
    Alachiotis N; Berger SA; Stamatakis A
    BMC Bioinformatics; 2012 Aug; 13():196. PubMed ID: 22876807
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Ancestral sequence alignment under optimal conditions.
    Hudek AK; Brown DG
    BMC Bioinformatics; 2005 Nov; 6():273. PubMed ID: 16293191
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Phylogeny-aware alignment with PRANK.
    Löytynoja A
    Methods Mol Biol; 2014; 1079():155-70. PubMed ID: 24170401
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Phylogeny-Aware Alignment with PRANK and PAGAN.
    Löytynoja A
    Methods Mol Biol; 2021; 2231():17-37. PubMed ID: 33289884
    [TBL] [Abstract][Full Text] [Related]  

  • 6. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.
    Liu K; Warnow TJ; Holder MT; Nelesen SM; Yu J; Stamatakis AP; Linder CR
    Syst Biol; 2012 Jan; 61(1):90-106. PubMed ID: 22139466
    [TBL] [Abstract][Full Text] [Related]  

  • 7. libgapmis: extending short-read alignments.
    Alachiotis N; Berger S; Flouri T; Pissis SP; Stamatakis A
    BMC Bioinformatics; 2013; 14 Suppl 11(Suppl 11):S4. PubMed ID: 24564250
    [TBL] [Abstract][Full Text] [Related]  

  • 8. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.
    Matsen FA; Kodner RB; Armbrust EV
    BMC Bioinformatics; 2010 Oct; 11():538. PubMed ID: 21034504
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.
    Blom J; Jakobi T; Doppmeier D; Jaenicke S; Kalinowski J; Stoye J; Goesmann A
    Bioinformatics; 2011 May; 27(10):1351-8. PubMed ID: 21450712
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
    Löytynoja A; Vilella AJ; Goldman N
    Bioinformatics; 2012 Jul; 28(13):1684-91. PubMed ID: 22531217
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Phylogenetic placement of metagenomic reads using the minimum evolution principle.
    Filipski A; Tamura K; Billing-Ross P; Murillo O; Kumar S
    BMC Genomics; 2015; 16 Suppl 1(Suppl 1):S13. PubMed ID: 25923672
    [TBL] [Abstract][Full Text] [Related]  

  • 12. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
    Löytynoja A; Goldman N
    BMC Bioinformatics; 2010 Nov; 11():579. PubMed ID: 21110866
    [TBL] [Abstract][Full Text] [Related]  

  • 13. SEPP: SATé-enabled phylogenetic placement.
    Mirarab S; Nguyen N; Warnow T
    Pac Symp Biocomput; 2012; ():247-58. PubMed ID: 22174280
    [TBL] [Abstract][Full Text] [Related]  

  • 14. On the quality of tree-based protein classification.
    Lazareva-Ulitsky B; Diemer K; Thomas PD
    Bioinformatics; 2005 May; 21(9):1876-90. PubMed ID: 15647305
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.
    Riesenfeld SJ; Pollard KS
    BMC Genomics; 2013 Jun; 14():419. PubMed ID: 23799973
    [TBL] [Abstract][Full Text] [Related]  

  • 16. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.
    Carbone I; White JB; Miadlikowska J; Arnold AE; Miller MA; Kauff F; U'Ren JM; May G; Lutzoni F
    Bioinformatics; 2017 Apr; 33(8):1160-1168. PubMed ID: 28003260
    [TBL] [Abstract][Full Text] [Related]  

  • 17. FastTree 2--approximately maximum-likelihood trees for large alignments.
    Price MN; Dehal PS; Arkin AP
    PLoS One; 2010 Mar; 5(3):e9490. PubMed ID: 20224823
    [TBL] [Abstract][Full Text] [Related]  

  • 18. LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference.
    Lawrence CJ; Zmasek CM; Dawe RK; Malmberg RL
    Bioinformatics; 2004 Aug; 20(12):1977-9. PubMed ID: 15044241
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood.
    Berger SA; Krompass D; Stamatakis A
    Syst Biol; 2011 May; 60(3):291-302. PubMed ID: 21436105
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Rapid alignment-free phylogenetic identification of metagenomic sequences.
    Linard B; Swenson K; Pardi F
    Bioinformatics; 2019 Sep; 35(18):3303-3312. PubMed ID: 30698645
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 13.