Sequence length bounds for resolving a deep phylogenetic divergence

Sequence length bounds for resolving a deep phylogenetic divergence.

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary relationship accurately depends on the model of sequence evolution, the substitution rate, divergence times and the method used to infer phylogenetic history. A...

Sequence-Length Requirements for Phylogenetic Methods

We study the sequence lengths required by neighbor-joining, greedy parsimony, and a phylogenetic reconstruction method (DCMNJ+MP) based on disk-covering and the maximum parsimony criterion. We use extensive simulations based on random birth-death trees, with controlled deviations from ultrametricity, to collect data on the scaling of sequence-length requirements for each of the three methods as...

REEF: Resolving Length Bias in Frequent Sequence Mining

Classic support based approaches efficiently address frequent sequence mining. However, support based mining has been shown to suffer from a bias towards short sequences. In this paper, we propose a method to resolve this bias when mining the most frequent sequences. In order to resolve the length bias we define norm-frequency, based on the statistical zscore of support, and use it to replace s...

REEF: Resolving Length Bias in Frequent Sequence Mining Using Sampling

Classic support based approaches efficiently address frequent sequence mining. However, support based mining has been shown to suffer from a bias towards short sequences. In this paper, we propose a method to resolve this bias when mining the most frequent sequences. In order to resolve the length bias we define norm-frequency, based on the statistical zscore of support, and use it to replace s...

Lower bounds of Copson type for the transpose of matrices on weighted sequence spaces