SPAGETI: Stabilizing Phylogenetic Assessment with Gene Evolutionary Tree Indices
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The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either supporting or conflicting with the consensus. Based on individual gene evolutionary tree, a recent study has demonstrated that this approach may result in incorrect solutions and developed the internode certainty (IC) heuristic for estimating the confidence of splits made on the consensus tree. Although an improvement, this heuristic neglects the differing rates of molecular evolution in individual genes. Here I develop an improved version of this method such that each gene is proportionally weighted based on its overall signal and specifically with the imbalanced signal for each node represented with gene tree.
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