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REGA HIV Subtyping Tool
Allows subtyping of Human Immunodeficiency Virus (HIV)-1 and 2 virus sequences. REGA HIV Subtyping Tool is a web application that uses phylogenetics methods for subtyping sequences. The software allows construction of phylogenetic trees representing each of the segments, bootscanning analysis and drawing of statistically supported conclusions relating to the virus genotype and its recombinant or non-recombinant nature. Users can classify of up to 1000 sequences in a single analysis.
Oxford HBV Subtyping Tool
Allows subtyping of Hepatitis B Virus (HBV) sequences. Oxford HBV Subtyping Tool is a web application that uses phylogenetics methods for subtyping sequences. The software allows construction of phylogenetic trees representing each of the segments, bootscanning analysis and drawing of statistically supported conclusions relating to the virus genotype and its recombinant or non-recombinant nature. Users can classify of up to 1000 sequences in a single analysis.
RDP4 / Recombination Detection Program
Implements an extensive array of methods for detecting and visualizing recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 can analyze up to 2500 sequences that can reach 10Mb. It is also applicable to the analysis of bacterial full-genome sequence datasets. It uses either fully automated mode from the command line interface or with a graphical user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.
GiRaF / Graph-incompatibility-based Reassortment Finder
Retrieves reassortments in a given collection of sequences. GiRaF employs data-mining techniques to recognize the set of isolates arising from a reassortment. It builds an incompatibility graph and mines it for phylogenetic discordances for comparing distributions of trees. This tool is useful for the study of viral datasets such as influenza. It can be used in combination with a ‘sliding window’ approach to find recombination breakpoints in large viral datasets.
LSD / Least-Square Dating
Fast dating algorithms, based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. LSD model is robust to uncorrelated violations of the molecular clock. These algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g., midpoint). Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra.
ViPTree
Helps to generate a "proteomic tree" of viral genome sequences based on genome-wide sequence similarities computed by tBLASTx. ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. This tool generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. It also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes.
ViralNet
Analyzes time series viral sequencing data. ViralNet can infer the evolutionary structure from a time series of sequencing experiments, which can also detect reassortment events, thus providing a method to help improve the understanding of within host evolution of viruses. ViralNet has been designed for three aims (i) to identify the presence of clones in mixed viral populations, (ii) to quantify the relative population sizes of the clones, and (iii) to describe underlying evolutionary structures, including reticulated evolution.
RotaC
Allows genotyping analysis of viral sequences. RotaC automates classification for group A rotaviruses. It can identify the genotype of a query sequence by using the nucleotide identity cut-off values. This tool employs a distance matrix based on pairwise alignments with the Needleman-Wunsch algorithm, and a phylogenetic tree based on the neighbour-joining algorithm. It is in agreement with the rotavirus classification strategy and guidelines as proposed by the Rotavirus Classification Working Group.
RV-Typer
An alignment-free method based on “return time distribution” (RTD) of amino acid residues in VP1 protein has been developed and implemented in the form of a web server, in view of the growing need for serotyping of Rhinoviruses (RV). RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2) to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods.
vConTACT / Viral CONTigs Automatic Clustering and Taxonomy
Allows classification of double-stranded DNA viruses that infect Archaea and Bacteria. vConTACT analyses are based on gene sharing network methods. It displays the extent of shared genes between genomes as edges. This tool enables large-scale, automated virus classification. VConTACT is integrated in a virus ecology-focused set of tools named iVirus. It enables any user to run the application simply by providing viral sequences alongside.
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