Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations...

A Minimum Spanning Tree Framework for Inferring Phylogenies

A Minimum Spanning Tree Framework for Inferring Phylogenies by Daniel Giannico Adkins Doctor of Philosophy in Computer Science University of California, Berkeley Professor Satish B. Rao, Chair This dissertation discusses how to write efficient, deterministic programs to infer phylogenetic trees. These programs are based on a theoretically optimal polynomial time algorithm. The programs are prac...

Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.

Phylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree. In the other, phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree. Here, we have compared these two app...

NEW DIRECTION IN FUZZY TREE AUTOMATA

In this paper, our focus of attention is the proper propagationof fuzzy degrees in determinization of $Nondeterministic$ $Fuzzy$$Finite$ $Tree$ $Automata$ (NFFTA). Initially, two determinizationmethods are introduced which have some limitations (one inbehavior preserving and other in type of fuzzy operations). Inorder to eliminate these limitations and increasing theefficiency of FFTA, we defin...

Moringa Oleifera, Miracle Tree