Table 2.

Analytical and visualization tools integrated into ViPR.

Tool Name	Function / Purpose
MUSCLE	Calculate a multiple sequence alignment (MSA) using either nucleotide or amino acid sequences
ReadSeq	Convert between various MSA formats
JalView	Visualize and modify nucleotide or amino acid MSA
FastME, PhyML, RAxML	Infer phylogenetic trees for nucleotide or amino acid sequences using either similarity or maximum likelihood-based algorithms
modelCompare, ProtTest	Determine which evolutionary model to use when constructing maximum likelihood trees
Archaeopteryx	Visualize, manipulate and decorate phylogenetic trees
Jmol	3D protein structure visualization / exploration
meta-CATS	Statistically compare groups of sequences to identify positions that significantly differ between them
BLAST	Identify similar nucleotide or amino acid sequences in a variety of custom ViPR databases
Sequence Variation Calculator	Compute the entropy present at each nucleotide or amino acid position at each position of user-defined groups of virus sequences
Short Peptide Identification Tool	Find short amino acid strings in target proteins using exact, fuzzy, or pattern matching
Genome Annotation Transfer Utility	Annotate a new genome sequence using an existing well-annotated reference genome
Primer3	Design PCR primers to amplify specific virus sequence(s) based on the data within ViPR