4.7 Article Data Paper

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research

Related references

Note: Only part of the references are listed.
Article Plant Sciences

Newly Recognized Diversity in Trochodendraceae from the Eocene of Western North America

Steven R. Manchester et al.

INTERNATIONAL JOURNAL OF PLANT SCIENCES (2018)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Article Biochemical Research Methods

Phased diploid genome assembly with single-molecule real-time sequencing

Chen-Shan Chin et al.

NATURE METHODS (2016)

Article Biochemical Research Methods

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

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

UniProt: a hub for protein information

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Andrew Adey et al.

GENOME RESEARCH (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

Joshua N. Burton et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemical Research Methods

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

Chen-Shan Chin et al.

NATURE METHODS (2013)

Article Biotechnology & Applied Microbiology

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

Daehwan Kim et al.

GENOME BIOLOGY (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

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

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Biochemistry & Molecular Biology

HMMER web server: interactive sequence similarity searching

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Erez Lieberman-Aiden et al.

SCIENCE (2009)

Article Biochemical Research Methods

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

Andrew D. Johnson et al.

BIOINFORMATICS (2008)

Review Genetics & Heredity

A unified classification system for eukaryotic transposable elements

Thomas Wicker et al.

NATURE REVIEWS GENETICS (2007)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

Zhao Xu et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes

Genis Parra et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

CAFE: a computational tool for the study of gene family evolution

T De Bie et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

InterProScan: protein domains identifier

E Quevillon et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemical Research Methods

De novo identification of repeat families in large genomes

AL Price et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

AUGUSTUS: a web server for gene finding in eukaryotes

M Stanke et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemical Research Methods

TigrScan and GlimmerHMM:: two open source ab initio eukaryotic gene-finders

WH Majoros et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

GeneWise and genomewise

E Birney et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

OrthoMCL: Identification of ortholog groups for eukaryotic genomes

L Li et al.

GENOME RESEARCH (2003)

Article Plant Sciences

First nuclear DNA c-values for 28 angiosperm genera

L Hanson et al.

ANNALS OF BOTANY (2003)

Article Biochemistry & Molecular Biology

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

J Castresana

MOLECULAR BIOLOGY AND EVOLUTION (2000)