Comparative transcriptomics of a complex of four European pine species

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Geographical patterns of nucleotide diversity and population differentiation in three closely related European pine species in thePinus mugocomplex

(2013) Witold Wachowiak et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

(2012) Limin Fu et al.   BIOINFORMATICS

The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps

(2012) E. Mosca et al.   MOLECULAR ECOLOGY

Sequence variation patterns along a latitudinal cline in Scots pine (Pinus sylvestris): signs of clinal adaptation?

(2012) Sonja T. Kujala et al.   Tree Genetics & Genomes

SNP markers trace familial linkages in a cloned population of Pinus taeda—prospects for genomic selection

(2012) Jaime Zapata-Valenzuela et al.   Tree Genetics & Genomes

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.)

(2011) WITOLD WACHOWIAK et al.   MOLECULAR ECOLOGY

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

(2010) Thomas L Parchman et al.   BMC GENOMICS

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

Cryptic hybrids between Pinus uncinata and P. sylvestris

(2010) ANNA K. JASIŃSKA et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2010) A. McKenna et al.   GENOME RESEARCH

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

(2010) W Wachowiak et al.   HEREDITY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Evolution of Genome Size and Complexity in Pinus

(2009) Alison M. Morse et al.   PLoS One

annot8r: GO, EC and KEGG annotation of EST datasets

(2008) Ralf Schmid et al.   BMC BIOINFORMATICS

Forests and Climate Change: Forcings, Feedbacks, and the Climate Benefits of Forests

(2008) G. B. Bonan   SCIENCE

Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.)

(2008) Witold Wachowiak et al.   Tree Genetics & Genomes