! See here for xml files for alignment and annotation of SARS-CoV-2 genomes
VIRULIGN is a tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins. We present a tutorial demonstrating VIRULIGN's functionality for three different pathogens (i.e., HIV-1, Dengue virus, Zika virus).
Please download releases for GNU/Linux, MacOS and Windows here. To install the download, just put the virulign binary in a directory that is in your PATH environment. To build VIRULIGN from source have a look at the BUILD.txt file.
For a detailed description of VIRULIGN and how to cite, please use:
Libin PJK, Deforche K, Abecasis AB and Theys K., (2018), VIRULIGN: fast codon-correct alignment and annotation of viral genomes, Bioinformatics, bty851, https://doi.org/10.1093/bioinformatics/bty851