ML as implemented in PhyML, version 3.0 [ 113, 114] was conducted using 100 random addition replicates and was based on a heuristic search using the tree bisection-reconnection (TBR) option; the best fit substitution model parameters were applied.
MP heuristic searches were performed by branch-swapping using the tree bisection-reconnection (TBR) algorithm, ACCTRAN character optimization, with all substitutions given equal weight, and with 10 random sequence addition replicates.
One thousand heuristic search replicates were done, using the tree bisection-reconnection branch-swapping algorithm and a random addition of taxa for each replicate, saving 100 trees per replicate.
Equal weighted maximum-parsimony (MP) analyses were performed with PAUP 4.0 beta [ 89] with a heuristic search using the TBR (tree-bisection-reconnection) algorithm for branch swapping.
Optimum trees were obtained with the heuristic method using the tree-bisection-reconnection branch-swapping option.
In the latter, starting trees were obtained using random sequence addition and swapped using the tree bisection reconnection algorithm.
Conditions for the ML analysis included starting trees obtained by stepwise addition, and branch swapping using the tree-bisection-reconnection (TBR) algorithm.
A consensus maximum parsimony tree was constructed with PAUP*, version 4.0 beta 10, with 10,000 bootstrap replicates using the tree-bisection-reconnection branch-swapping heuristic search algorithm.
The search for the best ML tree was done via a heuristic search using the tree bisection reconnection branch-swapping algorithm (TBR).
Maximum parsimony trees were created using the tree-bisection reconnection branch swapping method, and these were then used both to estimate model parameters and as a starting tree for the maximum likelihood analysis.
Maximum parsimony analysis of the combined data set was performed with Paup* v. 4.0 [ 64] using an equally weighted character matrix, heuristic searches using the tree-bisection-reconnection branch-swapping algorithm, and 100 random addition replicates.
