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121 ta ish

Ish: High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region

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

    Alexandros Stamatakis

    Maqola201469 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

    Maqola201428 iqtibos
    ABI

  3. WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas

    Stephen E. Fick, Robert J. Hijmans

    Maqola201725 iqtibos
    ABI

  4. The Sequence Alignment/Map format and SAMtools

    Heng Li, Bob Handsaker, Alec Wysoker +7

    Maqola200922 iqtibos
    ABI

  5. The variant call format and VCFtools

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

    Maqola201119 iqtibos
    ABI

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

    Shifu Chen, Yanqing Zhou, Yaru Chen +1

    Maqola201818 iqtibos
    ABI

  7. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

    Fumio Tajima

    Maqola198916 iqtibos
    ABI

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

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

    Maqola200715 iqtibos
    ABI

  9. Ancient Admixture in Human History

    Nick Patterson, Priya Moorjani, Yontao Luo +6

    Maqola201214 iqtibos
    ABI

  10. Fast and sensitive protein alignment using DIAMOND

    Benjamin Buchfink, Chao Xie, Daniel H. Huson

    Maqola201412 iqtibos
    ABI

  11. PAML 4: Phylogenetic Analysis by Maximum Likelihood

    Z. Yang

    Maqola200711 iqtibos
    ABI

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

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

    Maqola201510 iqtibos
    ABI

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

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

    Maqola20159 iqtibos
    ABI

  14. ANGSD: Analysis of Next Generation Sequencing Data

    Thorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus Nielsen

    Maqola20148 iqtibos
    ABI

  15. Inference of Population Structure using Dense Haplotype Data

    Daniel J. Lawson, Garrett Hellenthal, Simon Myers +1

    Maqola20127 iqtibos
    ABI

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

    Mihaela Pertea, Geo Pertea, Corina Antonescu +3

    Maqola20157 iqtibos
    ABI

  17. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

    Todd M. Lowe, Sean R. Eddy

    Maqola19977 iqtibos
    ABI

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

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

    Maqola20217 iqtibos
    ABI

  19. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

    Joseph K. Pickrell, Jonathan K. Pritchard

    Maqola20126 iqtibos
    ABI

  20. 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

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

    Brian Haas

    Maqola20036 iqtibos
    ABI

  22. Minimap2: pairwise alignment for nucleotide sequences

    Heng Li

    Maqola20185 iqtibos
    ABI

  23. OrthoFinder: phylogenetic orthology inference for comparative genomics

    David Emms, Steven Kelly

    Maqola20195 iqtibos
    ABI

  24. InterProScan 5: genome-scale protein function classification

    Philip Jones, David Binns, Hsin-Yu Chang +14

    Maqola20145 iqtibos
    ABI

  25. Population Genetic Consequences of Small Population Size: Implications for Plant Conservation

    Norman C. Ellstrand, Diane R. Elam

    Maqola19935 iqtibos
    ABI