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Viral sequence classification software tools | Phylogenomics

Viral sequence classification has wide applications in clinical, epidemiological, structural and functional categorization studies. Most existing approaches rely on an initial alignment step followed by classification based on phylogenetic or…
G T A T C G C T A
RDP4
Desktop

RDP4 Recombination Detection Program

Implements an extensive array of methods for detecting and visualizing…

Implements an extensive array of methods for detecting and visualizing recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP is capable of analyzing…

vConTACT
Desktop

vConTACT Viral CONTigs Automatic Clustering and Taxonomy

Allows classification of double-stranded DNA viruses that infect Archaea and…

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…

RV-Typer
Web

RV-Typer

An alignment-free method based on “return time distribution” (RTD) of amino…

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…

CASTOR
Web

CASTOR

Exploits robust machine learning classifiers for the classification of…

Exploits robust machine learning classifiers for the classification of sequences based on Restriction Fragment Length Polymorphism (RFLP) signatures. CASTOR allows the user to label nucleotide…

LSD
Desktop

LSD Least-Square Dating

Fast dating algorithms, based on a Gaussian model closely related to the…

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…

COMET
Web

COMET COntext-based Modeling for Expeditious Typing

An alignment-free typing algorithm for HIV-1 and other viruses (HCV). It is…

An alignment-free typing algorithm for HIV-1 and other viruses (HCV). It is freely available via an anonymous web-based interface and for academic usage as a stand-alone Java jar file by request to…

ViPTree
Web

ViPTree

Helps to generate a "proteomic tree" of viral genome sequences based…

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…

ViralNet
Desktop

ViralNet

Analyzes time series viral sequencing data. ViralNet can infer the evolutionary…

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…

BaTS
Desktop

BaTS Bayesian Tip-association Significance testing

A package to test for significant phylogeny-trait correlations. BaTS takes into…

A package to test for significant phylogeny-trait correlations. BaTS takes into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by…

SDT
Desktop

SDT Sequence Demarcation Tool

A free and easy to use program that allows classification of virus sequences…

A free and easy to use program that allows classification of virus sequences based on sequence pairwise identity. It takes as input a FASTA file of aligned or unaligned DNA or protein sequences and…

REGA HIV-1…
Web

REGA HIV-1 Subtyping Tool

This tool is designed to use phylogenetic methods in order to identify the…

This tool is designed to use phylogenetic methods in order to identify the subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods.

PASC
Web

PASC PAirwise Sequence Comparison

A web tool for analysis of pairwise identity distribution within viral…

A web tool for analysis of pairwise identity distribution within viral families. The identities are pre-computed for every pair within the families and with distribution plotted in a form of…

SCUEAL
Desktop
Web

SCUEAL

An algorithm to subtype and determine the mosaic structure of HIV-1 strains. A…

An algorithm to subtype and determine the mosaic structure of HIV-1 strains. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. This method…

jpHMM
Desktop
Web

jpHMM jumping profile Hidden Markov Model

A probabilistic approach to compare a sequence to a multiple alignment of a…

A probabilistic approach to compare a sequence to a multiple alignment of a sequence family. The jpHMM web server at GOBICS is a tool for the detection of recombinations in HIV-1 and hepatitis B…

MuLDAS
Web

MuLDAS

Classifies a query sequence based on the statistical genotype models learned…

Classifies a query sequence based on the statistical genotype models learned from the known sequences. MuLDAS utilizes full spectra of well characterized sequences as references, typically of an…

STAR
Web

STAR

Provides a fast and reliable means of assigning viral sequences to reference…

Provides a fast and reliable means of assigning viral sequences to reference groups using a distance-based protocol and an underlying statistical model. This implementation of STAR is designed for…

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