Learning with Parsimony for Large Scale Object Detection and Discovery

We examined phylogenetic relationships among the Namib day geckos (genus Rhoptropus) using DNA sequence data from the mitochondrial cytochrome b (cytb) and 16S ribosomal RNA genes. Maximum-parsimony analysis of the cytb, 16S, and combined (cytb/16S) datasets each recovered an identical single most-parsimonious tree, revealing two well-supported clades: (1) Rhoptropus afer 1 Rhoptropus bradfield...

The reliabilities of parsimony-based and likelihood-based methods for inferring positive selection at single amino acid sites were studied using the nucleotide sequences of human leukocyte antigen (HLA) genes, in which positive selection is known to be operating at the antigen recognition site. The results indicate that the inference by parsimony-based methods is robust to the use of different ...

Tuffley and Steel (Bull. Math. Biol. 59:581-607, 1997) proved that maximum likelihood and maximum parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been widely cited ever since. We show that small changes to the model assumptions suffice to make the two methods inequivalent. In p...

We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1alpha DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitoha...

Many forms of parsimony pressure are parametric, that is final fitness is a parametric model of the actual size and raw fitness values. The problem with parametric techniques is that they are hard to tune to prevent size from dominating fitness late in the evolutionary run, or to compensate for problem-dependent nonlinearities in the raw fitness function. In this paper we briefly discuss existi...

Article history: Available online 2 February 2012

The problem of finding a phylogeny with maximum parsimony is one of the main problems in computational biology. While it is impossible to search the possible tree space exhaustively for large data sets, most heuristic approaches try to search in the neighborhood of sub-optimal trees. The speed of computing a score for each tree (e.g. tree length or total number of character changes) is as impor...