Optimal Sequence Length Requirements for Phylogenetic Tree Reconstruction with Indels
STOC '19: 51st Annual ACM SIGACT Symposium on the Theory of Computing Phoenix AZ USA June, 2019(2019)
摘要
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to reconstruct the model tree with high probability. Traditionally, sequences mutate by substitution-only processes, although some recent work considers evolutionary processes with insertions and deletions. In this paper, we improve on previous work by giving a reconstruction algorithm that simultaneously has $O(\text{poly} \log n)$ sequence length and tolerates constant indel probabilities on each edge. Our recursively-reconstructed distance-based technique provably outputs the model tree when the model tree has $O(\text{poly} \log n)$ diameter and discretized branch lengths, allowing for the probability of insertion and deletion to be non-uniform and asymmetric on each edge. Our polylogarithmic sequence length bounds improve significantly over previous polynomial sequence length bounds and match sequence length bounds in the substitution-only models of phylogenetic evolution, thereby challenging the idea that many global misalignments caused by insertions and deletions when $p_{indel}$ is large are a fundamental obstruction to reconstruction with short sequences.
更多查看译文
关键词
Phylogenetic reconstruction,distance methods,sequence length requirements
AI 理解论文
溯源树
样例
生成溯源树,研究论文发展脉络
Chat Paper
正在生成论文摘要