Table 1.

Iterative Estimation of Candidate Models for Antibody Sequences.

Existing/Inferred Model	Model Used for Tree Inference	Initial sij	Initial πi	Log-Likelihood per Site
WAG	WAG	—	—	−45.396
LG	LG	—	—	−45.976
1	LG	LG	πMSA	−44.257
2	LG	LG	πLG	−44.231
3	1	1	πMSA	−44.239
4	1	1	${\stackrel{⌢}{\pi }}_1$	−44.237
5	2	2	πMSA	−44.246
6	2	2	${\stackrel{⌢}{\pi }}_2$	−44.263
7	3	3	πMSA	−44.273
8	3	3	${\stackrel{⌢}{\pi }}_3$	−44.239
9	4	4	πMSA	−44.257
10	4	4	${\stackrel{⌢}{\pi }}_4$	−44.247
11	WAG	WAG	πMSA	−44.237
12	WAG	WAG	πWAG	−44.249