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The influence of data partitioning was tested as well.
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Prior to concatenating the three sequence alignments, the congruency of data partitions was tested with a likelihood-based congruency test (α = 0.05; 10000 RELL bootstrap replicates) [57], using maximum likelihood (ML) topologies generated from individual gene analyses as well as the overall ML tree (see below).
Data partitions were tested for substitution saturation using a non-parametric statistical test implemented by DAMBE 4.5.47 [56].
Hence, CADM accurately detects completely incongruent matrices even when multiple data partitions are tested simultaneously.
Individual data partitions were tested for substitution saturation using a non-parametric statistical test based on an information entropy index [ 52] implemented in DAMBE 5.0.23 [ 53].
Congruence among data sets was tested with the partition homogeneity test [41].
The congruence of 18S and ITS1 data sets was tested using the partition homogeneity test implemented in PAUP∗4b10 [ 43].
Data partitioning is permitted via NEXUS format.
Partition homogeneity was tested in PAUP with 100 replicates.
Congruence of different data partitions (in this case genes) was tested with both the incongruence length difference (ILD) test [95] and Shimodaira-Hasegawa (S-H) test [96] as implemented in PAUP*4.0b.
In case of a single test object, LOO-CV resulted in the outer loop and 80 training and test data partitions were computed.
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