GUIDANCE: a web server for assessing alignment confidence scores
- Osnat Penn, Eyal Privman, Haim Ashkenazy, Giddy Landan, D. Graur, T. Pupko
- Computer Science, BiologyNucleic Acids Res.
- 22 May 2010
The GUIDANCE web-server is presented, a user-friendly, open access tool for the identification of unreliable alignment regions and measures the robustness of the alignment to guide-tree uncertainty.
Fundamentals of molecular evolution
An alignment confidence score capturing robustness to guide tree uncertainty.
- Osnat Penn, Eyal Privman, Giddy Landan, D. Graur, T. Pupko
- Biology, Computer ScienceMolecular biology and evolution
- 1 August 2010
It is shown that uncertainties in the guide tree used by progressive alignment methods are a major source of alignment uncertainty, and a novel method for quantifying the robustness of each alignment column to guide tree uncertainty is developed, based on the widely used bootstrap method for perturbing the phylogenetic tree.
The genome of the model beetle and pest Tribolium castaneum
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural…
Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.
It is shown that when branch lengths are unknown, it is better first to estimate branch lengths and then to estimate site-specific rates, and that a Bayesian approach is superior to maximum-likelihood under a wide range of conditions.
Alu-containing exons are alternatively spliced.
Results indicate that internal exons that contain an Alu sequence are predominantly, if not exclusively, alternatively spliced, and evolutionary events that cause a constitutive insertion of an AlU sequence into an mRNA are deleterious and selected against.
Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species
Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation.
A fast algorithm for joint reconstruction of ancestral amino acid sequences.
A dynamic programming algorithm for maximum-likelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic tree that scales linearly with the number of sequences and is applicable to practically any number of taxa.
ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information.
A novel methodology based on evolutionary relations among proteins as revealed by inferred phylogenetic trees is presented, and its capabilities for mapping binding sites in SH2 and PTB signaling domains are demonstrated.