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GUIDANCE: a web server for assessing alignment confidence scores
TLDR
We present the GUIDANCE web-server, a tool for assigning a confidence score for each residue, column and sequence in an alignment and for projecting these scores onto the MSA. Expand
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An alignment confidence score capturing robustness to guide tree uncertainty.
Multiple sequence alignment (MSA) is the basis for a wide range of comparative sequence analyses from molecular phylogenetics to 3D structure prediction. Sophisticated algorithms have been developedExpand
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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 agriculturalExpand
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Heads or tails: a simple reliability check for multiple sequence alignments.
The question of multiple sequence alignment quality has received much attention from developers of alignment methods. Less forthcoming, however, are practical measures for addressing alignmentExpand
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Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea
Archaebacterial halophiles (Haloarchaea) are oxygen-respiring heterotrophs that derive from methanogens—strictly anaerobic, hydrogen-dependent autotrophs. Haloarchaeal genomes are known to haveExpand
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Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids
Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. InformationExpand
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Early bioenergetic evolution
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganicExpand
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Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes.
Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated.Expand
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Endosymbiotic origin and differential loss of eukaryotic genes
TLDR
Lateral gene transfer from bacteria to eukaryotes is episodic, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria. Expand
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Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor.
Plastids are descended from a cyanobacterial symbiosis which occurred over 1.2 billion years ago. During the course of endosymbiosis, most genes were lost from the cyanobacterium's genome and manyExpand
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