cognac

Cognac (COre GeNe Alignment Concatenation) is an R package for for generating concatenated gene alignments. The main function identifies shared genes to be used as phylogenetic markers within the input set of genomes. Marker genes are aligned individually with mafft and concatenated into a single alignment for downstream phylogenetic analysis. The algorithm uses mutli-threading and several algorithmic tricks to improve speed and efficiency, which make cognac capable of generating core-gene alignments for thousands of genomes in only a few hours.