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Internal branch topology was validated via the interior branch test.
Note that interior branch test is more reliable for closely related sequences [33].
However, a branch test did show that it is significantly larger than ω along the background branches (p = 0.011, model 2 free ω vs. model 0).
The clustering of P. anserina sequences was well supported by the interior branch test, but only the two main internal nodes were well supported by bootstrapping analysis.
Phylogenetic trees were constructed using the neighbor-joining method and evaluated using the interior branch test method with MEGA software (version 4.0; available at: http: //www.megasoftware.net/).net/
The branch test did not indicate that ω along the foreground branch is significantly larger than 1 (model 2 free ω vs. model 2 ω = 1).
Similar(36)
Internal Branch Tests were conducted using 1000 replicates.
The branch tests applied above use an ω value averaged across the entire gene.
Inclusion of env V1-V2 domains coupled with internal branch tests for positive selection in our analysis was critical to uncover episodic selection within HIV-1 quasispecies.
We conducted bootstrap and interior branch tests available in the MEGA 3.1 package to assess statistical significance of the phylogenetic trees.
The reliability of the trees was evaluated by the interior branch tests with 1,000 replications.
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