Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Long-read sequence assembly of the gorilla genome

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Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

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

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Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don

(2015) H. Hirakawa et al.   DNA RESEARCH

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification

(2015) Changhe Wei et al.   MOLECULAR GENETICS AND GENOMICS

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

Spontaneous mutations of the UDP-glucose:flavonoid 3-O-glucosyltransferase gene confers pale- and dull-colored flowers in the Japanese and common morning glories

(2015) Yasumasa Morita et al.   PLANTA

High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species

(2015) Shota Sakaguchi et al.   Tree Genetics & Genomes

The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome

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Trimmomatic: a flexible trimmer for Illumina sequence data

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InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

BESST - Efficient scaffolding of large fragmented assemblies

(2014) Kristoffer Sahlin et al.   BMC BIOINFORMATICS

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

A chalcone isomerase-like protein enhances flavonoid production and flower pigmentation

(2014) Yasumasa Morita et al.   PLANT JOURNAL

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

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Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

The First 50 Plant Genomes

(2013) Todd P. Michael et al.   Plant Genome

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Development of EST-SSR markers of Ipomoea nil

(2012) Tong Ly et al.   BREEDING SCIENCE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

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

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Identification of r mutations conferring white flowers in the Japanese morning glory (Ipomoea nil)

(2008) Atsushi Hoshino et al.   JOURNAL OF PLANT RESEARCH

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One