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60 ta ish

Ish: Integrative multi-omics analysis traces the divergent evolution of Chinese and Vietnamese Cinnamon and elucidates the biosynthetic pathway of cinnamaldehyde derivatives

  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. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

    Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón

    Maqola200926 iqtibos
    ABI

  4. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

    Dong Zhang, Fangluan Gao, Ivan Jakovlić +4

    Maqola201925 iqtibos
    ABI

  5. Trimmomatic: a flexible trimmer for Illumina sequence data

    Anthony Bolger, Marc Lohse, Björn Usadel

    Maqola201423 iqtibos
    ABI

  6. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

    Bùi Quang Minh, Heiko A. Schmidt, Olga Chernomor +4

    Maqola202023 iqtibos
    ABI

  7. Fast model-based estimation of ancestry in unrelated individuals

    David H. Alexander, John Novembre, Kenneth Lange

    Maqola200919 iqtibos
    ABI

  8. The variant call format and VCFtools

    Petr Danecek, Adam Auton, Gonçalo R. Abecasis +10

    Maqola201119 iqtibos
    ABI

  9. PAML 4: Phylogenetic Analysis by Maximum Likelihood

    Z. Yang

    Maqola200711 iqtibos
    ABI

  10. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

    Aaron McKenna, Matthew G. Hanna, Eric Banks +8

    Maqola20109 iqtibos
    ABI

  11. Second-generation PLINK: rising to the challenge of larger and richer datasets

    Christopher Chang, Carson C. Chow, Laurent CAM Tellier +3

    Maqola20159 iqtibos
    ABI

  12. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

    Mihaela Pertea, Geo Pertea, Corina Antonescu +3

    Maqola20157 iqtibos
    ABI

  13. The domestication and evolutionary ecology of apples

    Amandine Cornille, Tatiana Giraud, M.J.M. Smulders +2

    Sharh maqola20137 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. HISAT: a fast spliced aligner with low memory requirements

    Daehwan Kim, Ben Langmead, Steven L. Salzberg

    Maqola20157 iqtibos
    ABI

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

    Guillaume Marçais, Carl Kingsford

    Maqola20116 iqtibos
    ABI

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

    Brian Haas

    Maqola20036 iqtibos
    ABI

  18. OrthoFinder: phylogenetic orthology inference for comparative genomics

    David Emms, Steven Kelly

    Maqola20195 iqtibos
    ABI

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

    Shujun Ou, Ning Jiang

    Maqola20174 iqtibos
    ABI

  20. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

    T. Rhyker Ranallo-Benavidez, Kamil S. Jaroň, Michael C. Schatz

    Maqola20204 iqtibos
    ABI

  21. Genomic variation in 3,010 diverse accessions of Asian cultivated rice

    Wensheng Wang, Ramil Mauleon, Zhiqiang Hu +68

    Maqola20184 iqtibos
    ABI

  22. De novo assembly of the <i>Aedes aegypti</i> genome using Hi-C yields chromosome-length scaffolds

    Olga Dudchenko, Sanjit Singh Batra, Arina D. Omer +8

    Maqola20174 iqtibos
    ABI

  23. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

    Neva C. Durand, Muhammad S. Shamim, Ido Machol +4

    Maqola20163 iqtibos
    ABI

  24. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

    Chi Zhang, Shan‐Shan Dong, Junyang Xu +2

    Maqola20182 iqtibos
    ABI

  25. Crop genetic erosion: understanding and responding to loss of crop diversity

    Colin K. Khoury, Stephen B. Brush, Denise E. Costich +12

    Sharh maqola20212 iqtibos
    ABI