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Larger sample size with a fixed denominator F-statistic or more bootstrap replicates (beyond 500) had minimal impact.
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Molecular Defined Operational Taxonomic Units (MOTU) [ 55, 56], were then defined as least inclusive terminal groups with 90% bootstrap support or more, using 1000 bootstrap replicates.
The two distal nodes with values >50% indicate that no other arrangement occurred more often in the bootstrap replicates, and that they are therefore strongly supported.
For ML, which is much more computer intensive, 100 bootstrap replicates were obtained.
Estimating likelihood parameter values and applying them to bootstrap replicates is more efficient then re-estimating the values for each bootstrap replicate [ 57].
For MRP, MP-EST and ASTRAL, using bestML input trees produced more accurate species trees than using bootstrap replicates, either as one input (All BS) or using MLBS.
By increasing the number of bootstrap replicates, one can obtain a more reliable measure of the variance of the phylogenetic bootstrap p-value [10].
For each network, 1000 bootstrap replicates were performed and summarized to obtain more robust and accurate consensus networks.
Ten thousand bootstrap replicates were performed.
Stability and robustness were validated with 1000 bootstrap replicates.
Node numbers are support based on 500 bootstrap replicates.
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