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100 ta ish

Ish: Haplotype-resolved genome of hexaploid Solanum nigrum: Insights into origin, evolution, and steroidal glycoalkaloid biosynthesis

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

    Kazutaka Katoh, Daron M. Standley

    Maqola201370 iqtibos
    ABI

  2. Trimmomatic: a flexible trimmer for Illumina sequence data

    Anthony Bolger, Marc Lohse, Björn Usadel

    Maqola201423 iqtibos
    ABI

  3. 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

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

    Shifu Chen, Yanqing Zhou, Yaru Chen +1

    Maqola201818 iqtibos
    ABI

  5. Fast and sensitive protein alignment using DIAMOND

    Benjamin Buchfink, Chao Xie, Daniel H. Huson

    Maqola201412 iqtibos
    ABI

  6. PAML 4: Phylogenetic Analysis by Maximum Likelihood

    Z. Yang

    Maqola200711 iqtibos
    ABI

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

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

    Maqola201510 iqtibos
    ABI

  8. Tandem repeats finder: a program to analyze DNA sequences

    Gary Benson

    Maqola199910 iqtibos
    ABI

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

    Mihaela Pertea, Daehwan Kim, Geo Pertea +2

    Maqola20168 iqtibos
    ABI

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

    LiMin Fu, Beifang Niu, Zhengwei Zhu +2

    Maqola20127 iqtibos
    ABI

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

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

    Maqola20197 iqtibos
    ABI

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

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

    Maqola20217 iqtibos
    ABI

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

    Guillaume Marçais, Carl Kingsford

    Maqola20116 iqtibos
    ABI

  14. Minimap2: pairwise alignment for nucleotide sequences

    Heng Li

    Maqola20185 iqtibos
    ABI

  15. AUGUSTUS: ab initio prediction of alternative transcripts

    Mario Stanke, O. Keller, Irfan Gunduz +3

    Maqola20065 iqtibos
    ABI

  16. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

    Brian J. Haas, Alexie Papanicolaou, Moran Yassour +20

    Maqola20135 iqtibos
    ABI

  17. OrthoFinder: phylogenetic orthology inference for comparative genomics

    David Emms, Steven Kelly

    Maqola20195 iqtibos
    ABI

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

    Xin Qiao, Qionghou Li, Hao Yin +5

    Maqola20194 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. WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

    Pengchuan Sun, Beibei Jiao, Yongzhi Yang +6

    Maqola20224 iqtibos
    ABI

  22. KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences

    Zhang Zhang

    Maqola20224 iqtibos
    ABI

  23. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

    Morgan N. Price, Paramvir Dehal, Adam P. Arkin

    Maqola20093 iqtibos
    ABI

  24. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

    Carlos P. Cantalapiedra, Ana Hernández-Plaza, Ivica Letunić +2

    Boshqa20213 iqtibos
    ABI

  25. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

    Mikita Suyama, David Torrents, Peer Bork

    Maqola20063 iqtibos
    ABI