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Bootstrap replicates were set to 1000 for all analyses.
Within bootscan analysis, step-size was set to 50 and bootstrap replicates were set to 80 due to file size restriction.
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The number of bootstrap replicates was set on 1,000 replicates.
The number of bootstrap replicates was set to 1000.
Bray-Curtis indices were used as similarity measures and 'unweighted pair-group averages' as the clustering algorithm; the number of bootstrap replicates was set to 10,000.
The number of bootstrap replicates was set to 1000 and phylogeny was constructed using Hasegawa-Kishino-Yano model, determined by MEGA 5.05 as the best fitting nucleotide substitution model.
Three thousand rapid bootstrap replicates were performed and all other parameters were set to default.
One hundred bootstrap replicates were generated for each data set with seqboot (Felsenstein 2005) and analyzed with FastTree as above.
To evaluate statistical significance of the phylogenetic trees 1,000 bootstrap replicates were generated from each data set using the PHYLIP program SEQBOOT.
1,000 bootstrap replicates were conducted on the data set using PAUP* 4.0b10 with maximum parsimony and using MEGA with neighbor-joining methods and the Poisson-corrected distance.
One hundred bootstrap replicates were generated from each data set and then subjected to ML bootstrap analysis with the LG+Γ+F model.
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