- BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs from OrthoDB.
- miRmap ranks potential protein-coding mRNA targets of miRNAs with a biologically meaningful criterion, the repression strength. The miRmap software combines thermodynamic, evolutionary, probabilistic and sequence-based features, which cover features from TargetScan, PITA, PACMIT, and miRanda; where the integrated model almost doubles the predictive power of TargetScan. The miRmap web application offers a user-friendly and feature-rich resource for browsing pre-computed miRNA targets for model organisms, as well as for predicting and ranking targets for user-submitted sequences.
- Newick Utilities are a suite of Unix shell tools for high-throughput phylogenomics that allow processing numerous or huge phylogenetic trees. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG), etc.
- ezVir is a computational pipeline for comprehensive screening of human viruses in high-throughput sequencing data with a user-friendly representation of bioinformatics analysis.
- OrthoDB is the hierarchical catalogue of orthologs that is now among the top three orthology resources worldwide, in both methodology and coverage. Gene orthology is the cornerstone of comparative genomics and gene function prediction. OrthoDB provides analysis of protein-coding genes from the increasing number of available genomes, identifying genes in current species that originated from a single gene of the last common ancestors along the species phylogeny. Hypothesizing on gene functions is instrumental for many studies in the field of molecular biology, and the concept of orthology, identifying “equivalent” genes across species, forms the basis for the most precise functional inferences.
- CEGA is a resource of Conserved Elements from Genomic Alignments. Harnessing the power of multiple species comparisons to detect genomic elements under purifying selection, CEGA provides a comprehensive set of CNCs (including the subclass of ultra-conserved elements – UCEs) at different radiations along the lineage of vertebrates. The web interface displays alignments, genomic locations, as well as biologically relevant data.
- ImmunoD is a resource that includes gene family assignments, annotations and phylogenetic data on immune-related insect genes.
- miROrtho provides predicted precursor miRNA genes in several animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.
- OrthoBlock is a resource of multiple-species ortholog-based synteny blocks across 45 arthropods, delineated at each radiation along the species phylogeny.
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