trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
TrimAl is a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses and can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized.
Whole-genome analyses resolve early branches in the tree of life of modern birds
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
eggNOG v4.0: nested orthology inference across 3686 organisms
The fourth version of the eggNOG database is presented, that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families.
The genome of melon (Cucumis melo L.)
- J. Garcia-Mas, A. Benjak, P. Puigdoménech
- BiologyProceedings of the National Academy of Sciences
- 2 July 2012
The data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber, and a low number of nucleotide-binding site–leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species.
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
Phylemon 2.0 offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results, and allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics).
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)
A reference genome sequence for sugar beet is presented as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions and provides evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses.
Immunity and other defenses in pea aphids, Acyrthosiphon pisum
It is suggested that several aspects of the aphid life style, such as their association with microbial symbionts, could facilitate survival without strong immune protection, and the traditional view of insect immunity may not be as broadly applicable as once thought.
ETE: a python Environment for Tree Exploration
The Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees, provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose.
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes
These genomic resources for aculeate wasps and first transcriptome-wide insights into the origin of castes bring us closer to a more general understanding of eusocial evolution and how phenotypic diversity arises from the same genome.