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Ish: Phylogenomics provides new insight into the phylogeny and diversification of Asian Lappula (Boraginaceae)

  1. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

    Fredrik Ronquist, Maxim Teslenko, Paul van der Mark +7

    Maqola201274 iqtibos
    ABI

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

    Kazutaka Katoh, Daron M. Standley

    Maqola201370 iqtibos
    ABI

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

    Alexandros Stamatakis

    Maqola201469 iqtibos
    ABI

  4. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

    Jian‐Jun Jin, Wen-Bin Yu, Jun-Bo Yang +4

    Maqola202041 iqtibos
    ABI

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

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

    Maqola201428 iqtibos
    ABI

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

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

    Maqola200926 iqtibos
    ABI

  7. Bandage: interactive visualization of <i>de novo</i> genome assemblies

    Ryan R. Wick, Mark B. Schultz, Justin Zobel +1

    Maqola201525 iqtibos
    ABI

  8. 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

  9. ModelFinder: fast model selection for accurate phylogenetic estimates

    Subha Kalyaanamoorthy, Bùi Quang Minh, Thomas K. F. Wong +2

    Maqola201724 iqtibos
    ABI

  10. Trimmomatic: a flexible trimmer for Illumina sequence data

    Anthony Bolger, Marc Lohse, Björn Usadel

    Maqola201423 iqtibos
    ABI

  11. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

    Ivica Letunić, Peer Bork

    Maqola202123 iqtibos
    ABI

  12. 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

  13. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

    Andrew Rambaut, Alexei J. Drummond, Dong Xie +2

    Maqola201818 iqtibos
    ABI

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

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

    Maqola201114 iqtibos
    ABI

  15. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

    Stéphane Guindon, Jean-François Dufayard, Vincent Lefort +3

    Maqola201010 iqtibos
    ABI

  16. CD-HIT: accelerated for clustering the next-generation sequencing data

    LiMin Fu, Beifang Niu, Zhengwei Zhu +2

    Maqola20127 iqtibos
    ABI

  17. CPGAVAS2, an integrated plastome sequence annotator and analyzer

    Linchun Shi, Haimei Chen, Mei Jiang +4

    Maqola20196 iqtibos
    ABI

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

    Guillaume Marçais, Carl Kingsford

    Maqola20116 iqtibos
    ABI

  19. PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

    Robert Lanfear, Paul B. Frandsen, April Wright +2

    Maqola20164 iqtibos
    ABI

  20. phytools: an R package for phylogenetic comparative biology (and other things)

    Liam J. Revell

    Maqola20114 iqtibos
    ABI

  21. 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

  22. Evolution of Gene Duplication in Plants

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

    Sharh maqola20163 iqtibos
    ABI

  23. Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus, Nothofagaceae)

    María Cristina Acosta, Andrea C. Premoli

    Maqola20093 iqtibos
    ABI

  24. The Chromosome Counts Database (<scp>CCDB</scp>) – a community resource of plant chromosome numbers

    Anna Rice, Lior Glick, Shiran Abadi +6

    Maqola20143 iqtibos
    ABI

  25. Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae)

    Judith Fehrer, Birgit Gemeinholzer, Jindřich Chrtek +1

    Maqola20063 iqtibos
    ABI