Phylo-k-mers databases for SHERPAS

SHERPAS is a new program to identify novel recombinant sequences in a large collection of viral sequences, and to provide a first estimate of their recombinant structure. SHERPAS is much faster than other softwares for recombination detection; its main feature is the use of a pre-computed database of \"phylogenetically-informed k-mers\" (or phylo-k-mers). The computation of this phylo-k-mer database is a heavy computational step, but it only needs to be executed once for a given reference alignment.

A phylo-k-mer database can be built from any reference alignment, and a phylogenetic tree built from that alignment, using RAPPAS2 (https://github.com/phylo42/rappas2). We propose here three ready-to-use databases, for three reference alignments:
-An alignment of 167 sequences of the pol region of the HIV genome, provided with the program SCUEAL, accessible at https://github.com/spond/SCUEAL/blob/master/data/pol2009.nex
-An alignment of 339 sequence of the whole HBV genome, provided with ...