36 research outputs found
The generalized Robinson-Foulds metric
The Robinson-Foulds (RF) metric is arguably the most widely used measure of
phylogenetic tree similarity, despite its well-known shortcomings: For example,
moving a single taxon in a tree can result in a tree that has maximum distance
to the original one; but the two trees are identical if we remove the single
taxon. To this end, we propose a natural extension of the RF metric that does
not simply count identical clades but instead, also takes similar clades into
consideration. In contrast to previous approaches, our model requires the
matching between clades to respect the structure of the two trees, a property
that the classical RF metric exhibits, too. We show that computing this
generalized RF metric is, unfortunately, NP-hard. We then present a simple
Integer Linear Program for its computation, and evaluate it by an
all-against-all comparison of 100 trees from a benchmark data set. We find that
matchings that respect the tree structure differ significantly from those that
do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable
Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects
Prior distributions on symmetric groups
coset spaces, permutation group, ranked data, terminal sets,
Bayesian analysis of order-statistics models for ranking data
data augmentation, Gibbs sampling, order-statistics model, ranking data,
The repeated insertion model for rankings: Missing link between two subset choice models
Approval voting, probabilistic choice models, probabilistic ranking models, subset choice,
Mixed-effects analyses of rank-ordered data
latent trait models, latent class analysis, probabilistic choice models, nominal categories model, Luce's choice model,
Concordance between two linear orders: The Spearman and Kendall coefficients revisited
Danielsâs inequality, Kendallâs tau, Linear order, Metric, Permutation, Spearmanâs rho,