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A maximum-likelihood phylogenetic tree with 100 bootstrap replicates was performed as for the Species tree.
A bootstrap analysis based on 150 bootstrap replicates was performed to assess robustness of individual clades.
Maximum likelihood analysis with 500 bootstrap replicates was performed with RAxML, version 7.0.4 [ 60].
A full heuristic search with 1,000 bootstrap replicates was performed to test the robustness of clade designations.
Maximum likelihood analysis with 100 bootstrap replicates was performed using PHYLIP3.6 with JTT distance and gamma = 0.5.
The maximum-likelihood (ML) phylogenetic analysis of multiple aligned sequences with bootstrap values for 100 bootstrap replicates was performed using PhyML (version 3.5) (3.5.
Similar(51)
To estimate support for the nodes, 1000 bootstrap replicates were performed and we retained only the values supporting the nodes accounting for more than 50% of the bootstrap replicates.
Ten thousand bootstrap replicates were performed.
A total of 1,000 bootstrap replicates were performed using neighbor-joining, and clades having >60% bootstrap support were identified (Fritz-Laylin et al. 2005).
In addition, 1000 bootstrap replicates were performed using the maximum-parsimony (MP) method, based on a branch-and-bound search by PAUP 4.0b10 (Swofford 2002).
A total of 1000 bootstrap replicates were performed for each maximum parsimony analyses.
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