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RDP: detection of recombination amongst aligned sequences
SUMMARY Recombination Detection Program (RDP) is a program that applies a pairwise scanning approach to the detection of recombination amongst a group of aligned DNA sequences. The software runs
RDP3: a flexible and fast computer program for analyzing recombination
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.
RDP4: Detection and analysis of recombination patterns in virus genomes
The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility, which can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.
RDP2: recombination detection and analysis from sequence alignments
UNLABELLED RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination
Detection of a SARS-CoV-2 variant of concern in South Africa
A newly arisen lineage of SARS-CoV-2 is described that is defined by eight mutations in the spike protein, including three substitutions at residues in its receptor-binding domain that may have functional importance.
SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these
Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses
The results suggest that genome regions encoding the structural proteins of both FMDV and other picornaviruses are functionally interchangeable modules, supporting recent proposals that the structural and nonstructural coding regions of the picornovirus are evolving largely independently of one another.
Revision of Begomovirus taxonomy based on pairwise sequence comparisons
Revised guidelines for the classification and nomenclature of begomoviruses are proposed and genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomviruses belonging to different species and strains, respectively.
Gene-wide identification of episodic selection.
A new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate, and a computationally inexpensive evidence metric for identifying sites subject to episodicpositive selection on any foreground branches.
Robust inference of positive selection from recombining coding sequences
A method is proposed that makes maximum likelihood inference of positive selection robust to the presence of recombination and decreases the false positive rate to acceptable levels while retaining high power.