Table 3.

Effect of ProGraphMSA+TR’s unit indel rate parameter on TR rate estimation

	Initial	1 iteration	Real
Parameter	0.1	0.00779	0.0083
Error	0.081 ± 0.036	−0.053 ± 0.027	−0.070 ± 0.028
Abs. error	0.225 ± 0.034	0.135 ± 0.025	0.138 ± 0.027
Parameter	0.1	0.342	0.417
Error	1.60 ± 0.11	1.42 ± 0.11	1.38 ± 0.11
Abs. error	1.67 ± 0.11	1.59 ± 0.10	1.54 ± 0.10

In the upper half of the table, the indel rate was chosen to be lower than ProGraph+TR’s default parameter. With an indel rate of 0.2 per unit and a unit length of 24 (GALA-LRR), the ideal setting for the parameter would be 0.0083. After one iteration with the wrong parameter, we estimated the rate parameter to 0.00779, which was already close to the true value and also yielded results, which were similar to those obtained with the true parameter value. The reported error and absolute error are in terms of TR unit indel counts and should be contrasted to the expected number of unit indels, which is 2 under the simulated tree length and unit count. In the lower half of the table, we used a unit indel rate of 10 and therefore expected on average 10 unit indels per tree. Again, after one iteration, the parameter was estimated sufficiently close to the true value.