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96 ta ish

Ish: The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation

  1. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

    Kazutaka Katoh, Daron M. Standley

    Maqola201370 iqtibos
    ABI

  2. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

    Alexandros Stamatakis

    Maqola201469 iqtibos
    ABI

  3. Fast and accurate short read alignment with Burrows–Wheeler transform

    Heng Li, Richard Durbin

    Maqola200921 iqtibos
    ABI

  4. fastp: an ultra-fast all-in-one FASTQ preprocessor

    Shifu Chen, Yanqing Zhou, Yaru Chen +1

    Maqola201818 iqtibos
    ABI

  5. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

    Michael I. Love, Wolfgang Huber, Simon Anders

    Maqola201414 iqtibos
    ABI

  6. Full-length transcriptome assembly from RNA-Seq data without a reference genome

    Manfred Grabherr, Brian J. Haas, Moran Yassour +18

    Maqola201114 iqtibos
    ABI

  7. Fast gapped-read alignment with Bowtie 2

    Ben Langmead, Steven L. Salzberg

    Maqola201211 iqtibos
    ABI

  8. PAML 4: Phylogenetic Analysis by Maximum Likelihood

    Z. Yang

    Maqola200711 iqtibos
    ABI

  9. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

    Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis +2

    Maqola201510 iqtibos
    ABI

  10. WGCNA: an R package for weighted correlation network analysis

    Peter Langfelder, Steve Horvath

    Maqola20089 iqtibos
    ABI

  11. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

    Mihaela Pertea, Daehwan Kim, Geo Pertea +2

    Maqola20168 iqtibos
    ABI

  12. Fast and accurate long-read alignment with Burrows–Wheeler transform

    Heng Li, Richard Durbin

    Maqola20107 iqtibos
    ABI

  13. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

    Daehwan Kim, Joseph M. Paggi, Chanhee Park +2

    Maqola20197 iqtibos
    ABI

  14. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

    Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng +2

    Maqola20217 iqtibos
    ABI

  15. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

    Brian J. Haas, Steven L. Salzberg, Wei Zhu +6

    Maqola20086 iqtibos
    ABI

  16. Flavonoids: biosynthesis, biological functions, and biotechnological applications

    Marı́a Lorena Falcone Ferreyra, Sebastián P. Rius, Paula Casati

    Maqola20126 iqtibos
    ABI

  17. A fast, lock-free approach for efficient parallel counting of occurrences of <i>k</i> -mers

    Guillaume Marçais, Carl Kingsford

    Maqola20116 iqtibos
    ABI

  18. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

    Brian Haas

    Maqola20036 iqtibos
    ABI

  19. MYB transcription factors in Arabidopsis

    Christian Dubos, Ralf Stracke, Erich Grotewold +3

    Sharh maqola20105 iqtibos
    ABI

  20. <tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

    Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth

    Maqola20095 iqtibos
    ABI

  21. A framework for variation discovery and genotyping using next-generation DNA sequencing data

    Mark A. DePristo, Eric Banks, Ryan Poplin +15

    Maqola20114 iqtibos
    ABI

  22. Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants

    Xin Qiao, Qionghou Li, Hao Yin +5

    Maqola20194 iqtibos
    ABI

  23. LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

    Shujun Ou, Ning Jiang

    Maqola20174 iqtibos
    ABI

  24. Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

    Jaime Huerta‐Cepas, Kristoffer Forslund, Luís Pedro Coelho +4

    Maqola20174 iqtibos
    ABI

  25. Gene finding in novel genomes

    Ian Korf

    Maqola20043 iqtibos
    ABI