checkV is a fully automated command-line pipeline for assessing the quality of
single-contig viral
genomes, including identification of host contamination for integrated proviruses, estimating
completeness for genome fragments, and identification of closed genomes.
SDT : A virus
classification tool based on pairwise sequence alignment and identity calculation.
MAFFT :
Multiple alignment program for amino acid or nucleotide sequences.
RAxML-ng is
a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
IQ-TREE :
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood.
VADR is a suite of
tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes
or gene families.
VAPiD is a
ultra-lightweight script for quickly annotating and preparing sequences of human viruses for sending to
NCBI Genbank.