Evolutionary distance estimation and fidelity of pair wise sequence alignment

BMC Bioinformatics

Table 1 Summary of all simulation conditions

Model	G+C%	Initial # Sites	κ	α	Insertion/Deletion Rate	Mean Indel Size	True distances simulated
JC	0.5	1000	n/a	n/a	100/40	4	0.02, 0.04, 0.06, 0.08, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0
HKY	0.6	1000	3.6	n/a	100/40	4	0.02, 0.04, 0.06, 0.08, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0
HKY + Γ	0.6	1000	3.6	1.0	100/40	4	0.02, 0.04, 0.06, 0.08, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0
HKY	0.6	100	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	200	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	300	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	400	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	500	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	1500	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	2000	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	5000	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	10000	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.6	1000	3.6	n/a	100/40	2	0.5, 1.0
HKY	0.6	1000	3.6	n/a	100/40	6	0.5, 1.0
HKY	0.6	1000	3.6	n/a	100/40	8	0.5, 1.0
HKY	0.6	1000	3.6	n/a	100/40	10	0.5, 1.0
HKY	0.6	1000	3.6	n/a	200/80	4	0.5, 1.0
HKY	0.6	1000	3.6	n/a	150/60	4	0.5, 1.0
HKY	0.6	1000	3.6	n/a	75/30	4	0.5, 1.0
HKY	0.6	1000	3.6	n/a	50/20	4	0.5, 1.0
HKY	0.7	1000	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.8	1000	3.6	n/a	100/40	4	0.5, 1.0
HKY	0.9	1000	3.6	n/a	100/40	4	0.5, 1.0
HKY + Γ	0.6	1000	3.6	0.25	100/40	4	0.5, 1.0
HKY + Γ	0.6	1000	3.6	0.5	100/40	4	0.5, 1.0

κ is the transition/transversion bias. α is the shape parameter for Γ-distributed intersite rate variation. Insertion/Deletion Rate is relative to the point mutation rate, i.e., a rate of 100/40 indicates 1 insertion every 100 point mutations and 1 deletion every 40 point mutations. Each simulation condition was replicated 1000 times.

ISSN: 1471-2105