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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh, Daron M. Standley
Maqola201370 iqtibos
ABI
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
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón
Maqola200926 iqtibos
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
Maqola202023 iqtibos
ABI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin
Maqola200921 iqtibos
ABI
Fast model-based estimation of ancestry in unrelated individuals
David H. Alexander, John Novembre, Kenneth Lange
Maqola200919 iqtibos
ABI
The variant call format and VCFtools
Petr Danecek, Adam Auton, Gonçalo R. Abecasis +10
Maqola201119 iqtibos
ABI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
R. C. Edgar
Maqola200418 iqtibos
ABI
fastp: an ultra-fast all-in-one FASTQ preprocessor
Shifu Chen, Yanqing Zhou, Yaru Chen +1
Maqola201818 iqtibos
ABI
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
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis +2
Maqola201510 iqtibos
ABI
TASSEL: software for association mapping of complex traits in diverse samples
Peter J. Bradbury, Zhiwu Zhang, Dallas E. Kroon +3
Maqola20079 iqtibos
ABI
Ultrafast Approximation for Phylogenetic Bootstrap
Bùi Quang Minh, Minh Anh Nguyen, A. von Haeseler
Maqola20139 iqtibos
ABI
APE: Analyses of Phylogenetics and Evolution in R language
Emmanuel Paradis, Julien Claude, Korbinian Strimmer
Maqola20048 iqtibos
ABI
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Guangchuang Yu, Li-Gen Wang, Yanyan Han +1
Maqola20128 iqtibos
ABI
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim, Joseph M. Paggi, Chanhee Park +2
Maqola20197 iqtibos
ABI
Principal components analysis corrects for stratification in genome-wide association studies
Alkes L. Price, Nick J. Patterson, Robert M. Plenge +3
Maqola20066 iqtibos
ABI
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
AUGUSTUS: ab initio prediction of alternative transcripts
Mario Stanke, O. Keller, Irfan Gunduz +3
Maqola20065 iqtibos
ABI
Interactive Tree Of Life (iTOL) v4: recent updates and new developments
Ivica Letunić, Peer Bork
Maqola20194 iqtibos
ABI
The MEME Suite
Timothy L. Bailey, James Johnson, Charles E. Grant +1
Maqola20154 iqtibos
ABI
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
Xin Qiao, Qionghou Li, Hao Yin +5
Maqola20194 iqtibos
ABI
Gene finding in novel genomes
Ian Korf
Maqola20043 iqtibos
ABI
ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments
Zhang Zhang, Jingfa Xiao, Jiayan Wu +4
Maqola20123 iqtibos
ABI
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
Zhigang Xu, Hao Wang
Maqola20073 iqtibos
ABI