Table 2.

Topologies supported

Dataset	Preferred topology
	LD	NJP	NJK	NJD	MP	ML	QP
8308-site	–	1	1	1	2	2	2
7474-site	1	1	1	1	4	2	3
5153-site	–	1	1	1	2	6	2
4139-site	8	1	1	5	4	7	3

^*T1–T8 shown in Fig. 4, topologies indicate LD, bootstrap consensus topology (NJP, NJK, NJD, MP) or ML result (ML, QP).

^† LD performed without gapped sites only.