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RDP3: a flexible and fast computer program for analyzing recombination
- D. Martin, P. Lemey, M. Lott, V. Moulton, D. Posada, P. Lefeuvre
- Biology, Computer ScienceBioinform.
- 26 August 2010
RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments that includes four new recombination analysis methods, new tests for recombination hot-spots, and a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction.
Neighbor-net: an agglomerative method for the construction of phylogenetic networks.
Neighbor-Net is presented, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei and can quickly produce detailed and informative networks for several hundred taxa.
Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis.
Deep-sequencing, computational and molecular methods are used to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues, and it is found that many known and new mi RNAs showed tissue-specific expression.
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.
This study uses high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato fruit and leaf and raises the possibility that fruit development and ripening may be under miRNA regulation.
NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks
NeighborNet is introduced, a network construction and data representation method that combines aspects of the neighbor joining (NJ) and SplitsTree and can be used to represent multiple phylogenetic hypotheses simultaneously, or to detect complex evolutionary processes like recombination, lateral transfer and hybridization.
Maximal Energy Graphs
It is shown that if G is a graph on n vertices, then E(G)@?n21+n must hold, and an infinite family of graphs for which this bound is sharp is given.
A toolkit for analysing large-scale plant small RNA datasets
- S. Moxon, F. Schwach, T. Dalmay, D. MacLean, D. Studholme, V. Moulton
- 1 October 2008
A suite of web-based tools for processing plant small RNA datasets can be used to identify micro RNAs and their targets, compare expression levels in s RNA loci, and find putative trans-acting siRNA loci.
The impact of temperature on marine phytoplankton resource allocation and metabolism
This approach indicates that temperature plays a previously unrecognized, critical role in resource allocation and marine phytoplankton elemental ratios, with implications for biogeochemical cycling.
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing
A new software tool called PAREsnip is described that allows users to search for potential targets of all sRNAs obtained from high-throughput sequencing experiments, to facilitate large-scale identification of sRNA targets, allowing us to discover regulatory interaction networks.
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets
The UEA sRNA workbench is presented, a suite of tools that is a successor to the web-based UEE sRNA Toolkit, but in downloadable format and with several enhanced and additional features.