Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

Genome-wide identification and analysis of the MADS-box gene family in apple

(2015) Yi Tian et al.   GENE

De novo transcriptome sequencing in Ficus hirta Vahl. (Moraceae) to investigate gene regulation involved in the biosynthesis of pollinator attracting volatiles

(2015) Hui Yu et al.   Tree Genetics & Genomes

Diversity in the breadfruit complex (Artocarpus, Moraceae): genetic characterization of critical germplasm

(2015) Nyree Zerega et al.   Tree Genetics & Genomes

Chloroplast Microsatellite Markers forArtocarpus(Moraceae) Developed from Transcriptome Sequences

(2015) Elliot M. Gardner et al.   Applications in Plant Sciences

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Gene Prediction and Annotation inPenstemon(Plantaginaceae): A Workflow for Marker Development from Extremely Low-Coverage Genome Sequencing

(2014) Paul D. Blischak et al.   Applications in Plant Sciences

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Assessing De Novo transcriptome assembly metrics for consistency and utility

(2013) Shawn T O’Neil et al.   BMC GENOMICS

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft genome sequence of the mulberry tree Morus notabilis

(2013) Ningjia He et al.   Nature Communications

Development of Microsatellite Loci inArtocarpus altilis(Moraceae) and Cross-Amplification in Congeneric Species

(2013) Colby Witherup et al.   Applications in Plant Sciences

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

(2012) Limin Fu et al.   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

The draft genome and transcriptome of Cannabis sativa

(2011) Harm van Bakel et al.   GENOME BIOLOGY

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS