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Ish: Chromosome-level genome assembly of <i>Pinus massoniana</i> provides insights into conifer adaptive evolution

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

    Kazutaka Katoh, Daron M. Standley

    MaqolaOchiq kirish201397 iqtibos
    ABI

  2. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

    Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler +1

    MaqolaOchiq kirish201431 iqtibos
    ABI

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

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

    MaqolaOchiq kirish200931 iqtibos
    ABI

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

    Heng Li, Richard Durbin

    MaqolaOchiq kirish200929 iqtibos
    ABI

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

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

    MaqolaOchiq kirish202029 iqtibos
    ABI

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

    Shifu Chen, Yanqing Zhou, Yaru Chen +1

    MaqolaOchiq kirish201828 iqtibos
    ABI

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

    David H. Alexander, John Novembre, Kenneth Lange

    MaqolaOchiq kirish200923 iqtibos
    ABI

  8. The variant call format and VCFtools

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

    MaqolaOchiq kirish201121 iqtibos
    ABI

  9. MUSCLE: multiple sequence alignment with high accuracy and high throughput

    R. C. Edgar

    MaqolaOchiq kirish200421 iqtibos
    ABI

  10. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

    Shaun Purcell, Benjamin M. Neale, Katherine EO Todd-Brown +8

    MaqolaOchiq kirish200720 iqtibos
    ABI

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

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

    MaqolaOchiq kirish201512 iqtibos
    ABI

  12. TASSEL: software for association mapping of complex traits in diverse samples

    Peter J. Bradbury, Zhiwu Zhang, Dallas E. Kroon +3

    MaqolaOchiq kirish200711 iqtibos
    ABI

  13. Ultrafast Approximation for Phylogenetic Bootstrap

    Bùi Quang Minh, Minh Anh Nguyen, A. von Haeseler

    MaqolaOchiq kirish201310 iqtibos
    ABI

  14. APE: Analyses of Phylogenetics and Evolution in R language

    Emmanuel Paradis, Julien Claude, Korbinian Strimmer

    MaqolaOchiq kirish20049 iqtibos
    ABI

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

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

    MaqolaOchiq kirish20199 iqtibos
    ABI

  16. clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

    Guangchuang Yu, Li-Gen Wang, Yanyan Han +1

    MaqolaOchiq kirish20128 iqtibos
    ABI

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

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

    MaqolaOchiq kirish20087 iqtibos
    ABI

  18. Principal components analysis corrects for stratification in genome-wide association studies

    Alkes L. Price, Nick J. Patterson, Robert M. Plenge +3

    Maqola20066 iqtibos
    ABI

  19. AUGUSTUS: ab initio prediction of alternative transcripts

    Mario Stanke, O. Keller, Irfan Gunduz +3

    MaqolaOchiq kirish20066 iqtibos
    ABI

  20. Evolution of Gene Duplication in Plants

    Nicholas Panchy, Melissa D. Lehti‐Shiu, Shin‐Han Shiu

    Sharh maqolaOchiq kirish20165 iqtibos
    ABI

  21. Interactive Tree Of Life (iTOL) v4: recent updates and new developments

    Ivica Letunić, Peer Bork

    MaqolaOchiq kirish20194 iqtibos
    ABI

  22. The MEME Suite

    Timothy L. Bailey, James Johnson, Charles E. Grant +1

    MaqolaOchiq kirish20154 iqtibos
    ABI

  23. Trends, Rhythms, and Aberrations in Global Climate 65 Ma to Present

    James C. Zachos, Mark Pagani, Lisa C. Sloan +2

    Sharh maqola20014 iqtibos
    ABI

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

    Xin Qiao, Qionghou Li, Hao Yin +5

    MaqolaOchiq kirish20194 iqtibos
    ABI

  25. Sensitive protein alignments at tree-of-life scale using DIAMOND

    Benjamin Buchfink, Klaus Reuter, Hajk‐Georg Drost

    MaqolaOchiq kirish20214 iqtibos
    ABI