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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. Expand
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RDP2: recombination detection and analysis from sequence alignments
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 methods, including GENECONV, BOOTSCAN, MAXIMUM chi(2), CHIMAERA and SISTER SCANNING. Expand
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RDP4: Detection and analysis of recombination patterns in virus genomes
RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, andExpand
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A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.
We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification of nonrecombinant referenceExpand
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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 theseExpand
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Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses
ABSTRACT Foot-and-mouth disease virus (FMDV) is thought to evolve largely through genetic drift driven by the inherently error-prone nature of its RNA polymerase. There is, however, increasingExpand
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Revision of Begomovirus taxonomy based on pairwise sequence comparisons
Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that isExpand
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Gene-wide identification of episodic selection.
We present BUSTED, 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. BUSTEDExpand
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Robust inference of positive selection from recombining coding sequences
We propose a method that makes maximum likelihood inference of positive selection robust to the presence of recombination. Expand
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Evidence of Unique Genotypes of Beak and Feather Disease Virus in Southern Africa
ABSTRACT Psittacine beak and feather disease (PBFD), caused by Beak and feather disease virus (BFDV), is the most significant infectious disease in psittacines. PBFD is thought to have originated inExpand
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