SPAGETI: Stabilizing Phylogenetic Assessment with Gene Evolutionary Tree Indices
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.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
Comparing the topology of phylogenetic network generators
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more co…
What can phylogenetic metrics tell us about useful diversity in evolutionary algorithms?
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary c…
DiversityEvolutionary AlgorithmsNonbinary tree-based phylogenetic networks
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by…
Dimensions of Level-1 Group-Based Phylogenetic Networks
Phylogenetic networks represent evolutionary histories of sets of taxa where horizontal evolution or hybridization has occurred. Placing a Markov model of evolution on a phylogenetic network gives a model that is particu…
Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure
Evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution, and have been hypothesized to…