Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the
(A) Gap-filling: a gap (with N’s) is replaced with the corresponding sequence (e.g., ATGCTA). (B) Splitting: A contig is split into two sequences at the zero-coverage position. (C) Representative sequ