Работы, на которые ссылается эта работа

Работ: 100

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh, Daron M. Standley
Статья2013Цитирований: 70
ABI
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony Bolger, Marc Lohse, Björn Usadel
Статья2014Цитирований: 23
ABI
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Bùi Quang Minh, Heiko A. Schmidt, Olga Chernomor +4
Статья2020Цитирований: 23
ABI
fastp: an ultra-fast all-in-one FASTQ preprocessor
Shifu Chen, Yanqing Zhou, Yaru Chen +1
Статья2018Цитирований: 18
ABI
Fast and sensitive protein alignment using DIAMOND
Benjamin Buchfink, Chao Xie, Daniel H. Huson
Статья2014Цитирований: 12
ABI
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Z. Yang
Статья2007Цитирований: 11
ABI
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis +2
Статья2015Цитирований: 10
ABI
Tandem repeats finder: a program to analyze DNA sequences
Gary Benson
Статья1999Цитирований: 10
ABI
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
Mihaela Pertea, Daehwan Kim, Geo Pertea +2
Статья2016Цитирований: 8
ABI
CD-HIT: accelerated for clustering the next-generation sequencing data
LiMin Fu, Beifang Niu, Zhengwei Zhu +2
Статья2012Цитирований: 7
ABI
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim, Joseph M. Paggi, Chanhee Park +2
Статья2019Цитирований: 7
ABI
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Haoyu Cheng, Gregory T. Concepcion, Xiaowen Feng +2
Статья2021Цитирований: 7
ABI
A fast, lock-free approach for efficient parallel counting of occurrences of <i>k</i> -mers
Guillaume Marçais, Carl Kingsford
Статья2011Цитирований: 6
ABI
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
Статья2018Цитирований: 5
ABI
AUGUSTUS: ab initio prediction of alternative transcripts
Mario Stanke, O. Keller, Irfan Gunduz +3
Статья2006Цитирований: 5
ABI
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
Статья2013Цитирований: 5
ABI
OrthoFinder: phylogenetic orthology inference for comparative genomics
David Emms, Steven Kelly
Статья2019Цитирований: 5
ABI
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
Xin Qiao, Qionghou Li, Hao Yin +5
Статья2019Цитирований: 4
ABI
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons
Shujun Ou, Ning Jiang
Статья2017Цитирований: 4
ABI
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
T. Rhyker Ranallo-Benavidez, Kamil S. Jaroň, Michael C. Schatz
Статья2020Цитирований: 4
ABI
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
Pengchuan Sun, Beibei Jiao, Yongzhi Yang +6
Статья2022Цитирований: 4
ABI
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences
Zhang Zhang
Статья2022Цитирований: 4
ABI
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Morgan N. Price, Paramvir Dehal, Adam P. Arkin
Статья2009Цитирований: 3
ABI
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
Carlos P. Cantalapiedra, Ana Hernández-Plaza, Ivica Letunić +2
Другое2021Цитирований: 3
ABI
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Mikita Suyama, David Torrents, Peer Bork
Статья2006Цитирований: 3
ABI