Divergence and adaptive evolution of the gibberellin oxidase genes in plants

Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies

(2014) Eli Levy Karin et al.   MOLECULAR BIOLOGY AND EVOLUTION

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

Evolution and diversity of the 2-oxoglutarate-dependent dioxygenase superfamily in plants

(2014) Yosuke Kawai et al.   PLANT JOURNAL

Gibberellin metabolism in Vitis vinifera L. during bloom and fruit-set: functional characterization and evolution of grapevine gibberellin oxidases

(2013) Lisa Giacomelli et al.   JOURNAL OF EXPERIMENTAL BOTANY

Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary

(2013) Rachael A. Bay et al.   JOURNAL OF MOLECULAR EVOLUTION

Functional characterization of gibberellin oxidases from cucumber, Cucumis sativus L.

(2013) Maria João Pimenta Lange et al.   PHYTOCHEMISTRY

Functional Divergence and Convergent Evolution in the Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenases of Diverse Eukaryotic Algae

(2013) Daniel Gaston et al.   PLoS One

Adaptive evolution of the chrysanthemyl diphosphate synthase gene involved in irregular monoterpene metabolism

(2012) Ping-Li Liu et al.   BMC EVOLUTIONARY BIOLOGY

A phylogenetic mixture model for the identification of functionally divergent protein residues

(2011) Daniel Gaston et al.   BIOINFORMATICS

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Natural diversity and adaptation in plant secondary metabolism

(2011) Juergen Kroymann   CURRENT OPINION IN PLANT BIOLOGY

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

(2011) Eyal Privman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular evolution of the duplicated TFIIAγ genes in Oryzeae and its relatives

(2010) Hong-Zheng Sun et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary analysis of three gibberellin oxidase genesin rice, Arabidopsis, and soybean

(2010) Fengming Han et al.   GENE

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

(2010) Daniel Seeliger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

Evolutionary rate patterns of the Gibberellin pathway genes

(2009) Yan-hua Yang et al.   BMC EVOLUTIONARY BIOLOGY

QMEAN server for protein model quality estimation

(2009) Pascal Benkert et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Diversity, regulation, and evolution of the gibberellin biosynthetic pathway in fungi compared to plants and bacteria

(2009) Christiane Bömke et al.   PHYTOCHEMISTRY

Characterization of gibberellin 20-oxidases in the citrus hybrid Carrizo citrange

(2009) L. Huerta et al.   TREE PHYSIOLOGY

Gibberellin Metabolism and its Regulation

(2008) Shinjiro Yamaguchi   Annual Review of Plant Biology

Characterization and prediction of residues determining protein functional specificity

(2008) John A. Capra et al.   BIOINFORMATICS

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

(2008) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY

Genomic insights in moss gibberellin biosynthesis

(2008) Aldwin Anterola et al.   BRYOLOGIST

A Novel Class of Gibberellin 2-Oxidases Control Semidwarfism, Tillering, and Root Development in Rice

(2008) S.-F. Lo et al.   PLANT CELL

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Hormonal regulation in green plant lineage families

(2008) M. M. Johri   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS