Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins

Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions

(2014) Cymon J. Cox et al.   SYSTEMATIC BIOLOGY

Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

(2012) Tal Dagan et al.   Genome Biology and Evolution

Resolving Discrepancy between Nucleotides and Amino Acids in Deep-Level Arthropod Phylogenomics: Differentiating Serine Codons in 21-Amino-Acid Models

(2012) Andreas Zwick et al.   PLoS One

Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

(2012) D. C. Price et al.   SCIENCE

Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study

(2012) Omar Rota-Stabelli et al.   SYSTEMATIC BIOLOGY

Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes

(2011) Cheong Xin Chan et al.   CURRENT BIOLOGY

The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis

(2011) Steven Ball et al.   JOURNAL OF EXPERIMENTAL BOTANY

Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria

(2011) Alexis Criscuolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Dating the cyanobacterial ancestor of the chloroplast

(2010) Luisa I Falcón et al.   ISME Journal

Differential Gene Retention in Plastids of Common Recent Origin

(2010) A. Reyes-Prieto et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Is convergence surprising? An examination of the frequency of convergence in simulated datasets

(2008) C. Tristan Stayton   JOURNAL OF THEORETICAL BIOLOGY

Genes of Cyanobacterial Origin in Plant Nuclear Genomes Point to a Heterocyst-Forming Plastid Ancestor

(2008) O. Deusch et al.   MOLECULAR BIOLOGY AND EVOLUTION

The archaebacterial origin of eukaryotes

(2008) C. J. Cox et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Symbiosis and the Birth of the Plant Kingdom

(2007) P. Deschamps et al.   MOLECULAR BIOLOGY AND EVOLUTION