Viral sequence classification software tools | Phylogenomics data analysis
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 statistical algorithms.
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.
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.
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.
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 aligns every unique pair of sequences, calculates pairwise similarity scores, and displays a colour coded matrix of these scores. It also produces both a plot of these pairwise identity scores and text files containing analysis results.
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 virus (HBV) genomes.
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 is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods.
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 Bayesian phylogenetics programs. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.