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On the other hand, herein partitioned analyses always obtained the same topology as non-partitioned ML analyses, and PHASE analyses did not resolve incongruence either.
Partitioned analyses also reveal that pelvic characters alone are not sufficient to recover a monophyletic Sulidae.
Partitioned analyses were conducted by partitioning sites based on mixed model analysis.
Partitioned analyses were conduced using MrBayes for BI and a pre-release version of RAxML for ML, as described above.
Partitioned Analyses were conduced using MrBayes for BI and a pre-release version of RAxML [53] for ML.
Partitioned analyses might reduce potential model misspecifications and might yield congruent topologies.
Bayesian partitioned analyses often had fewer parameters, as MrBayes can implement simpler models than the GTR+Γ (e.g. HKY).
Partitioned analyses with Γ-distributed rate heterogeneity over sites were performed using RAxML version 7.4.2 (Stamatakis 2006, 2012).
Partitioned analyses were performed for ML and BI, with 16 partitions for the mitochondrial and 9 for the nuclear datasets.
Partitioned analyses were performed with GARLI, version 2.0 [ 49] and MrBayes, version 3.2 [ 50] that allowed the overall rate to be different across partitions (rbcLS, COI, and ITS).
Partitioned analyses using rRNA models as applied in our analysis, have been reported to result in better-supported topologies (for sponges: [ 13, 14]).
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