Algorithms in Bioinformatics
- Computer Science, BiologyLecture Notes in Computer Science
A new method and a preliminary system is presented that directly incorporates inter-dependencies among locations into the multiple-location-prediction process, using a collection of Bayesian network classifiers and results are significantly higher than those obtained by classifiers that do not use inter- dependency.
Statistical approaches to phylogenetic networks, recombination and testing of incongruence
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Is there a justification for differential a priori weighting in coding sequences? A case study from rbcL and Apocynaceae s.l.
- BiologySystematic biology
It is shown there is no significant difference in performance between parsimony-informative sites constrained by function in the enzyme, and sites that are not, and the substitutions in third-codon position performed significantly better than those in first and second.
Phylogenetic frameworks: towards a firmer foundation for the comparative approach
It is concluded that taxonomic congruence is preferable to character Congruence for estimating accuracy of phylogenetic hypotheses, and the combinable components approach, when preceded by application of rigorous statistical manipulations, is most appropriate.
A MULTILOCUS GENEALOGICAL APPROACH TO PHYLOGENETIC SPECIES RECOGNITION IN THE MODEL EUKARYOTE NEUROSPORA
- BiologyEvolution; international journal of organic evolution
Not only were phylogenetic criteria superior to traditional reproductive compatibility criteria in revealing the full species diversity of Neurospora, but also significant phylogenetic subdivisions were detected within some species.
New clades of euthyneuran gastropods (Mollusca) from 28S rRNA sequences.
- BiologyMolecular phylogenetics and evolution
Morphological characters which support the new clades obtained here are discussed and first molecular confirmation of monophylies of Hygrophila, including Chilina, Acteonoidea, and Sacoglossa, which include both shell-bearing species and slugs are discussed.
Measuring Topological Congruence by Extending Character Techniques
- MathematicsCladistics : the international journal of the Willi Hennig Society
A measure of topological congruence which is an extension of the Mickevich–Farris character incongruence metric (i.e., ILD; Mickevich and Farris, 1981) is proposed. Group inclusion characters (1 =…
ON CONSENSUS, COLLAPSIBILITY, AND CLADE CONCORDANCE
The clade concordance index is proposed, which employs the consensus tree length to measure inter‐cladogram character conflict for all characters among a set of cladograms.
TreeTerminus - Creating transcript trees using inferential replicate counts
- Computer SciencebioRxiv
TreeTerminus is introduced, a data-driven approach for grouping transcripts into a tree structure where leaves represent individual transcripts and internal nodes represent an aggregation of a transcript set, and an improved performance compared to transcripts and other methods under several different metrics is observed.
- BiologyCladistics : the international journal of the Willi Hennig Society
Several methods to reconcile multiple such graphs are presented and discussed here, extending existing consensus and supertree techniques to form a set of phylogenetic supergraph methods.
SHOWING 1-10 OF 18 REFERENCES
A View of Some Consensus Methods for Trees
The study of consensus is important, assuming most participants of this conference are aware that the topic has recently been drawing considerable attention.
- Mathematics, Computer Science
A method is presented, called majority rule, which can be used to define a consensus of these classifications, and some mathematical properties of this consensus tree are discussed.
Analysis of Taxonomic Congruence among Morphological, Ecological, and Biogeographic Data Sets for the Leptopodomorpha (Hemiptera)
The minimum length Wagner tree and a published scheme of Polhemus show maximum congruence and a classification isomorphic with the Wagner tree is proposed as the one which should be used for future studies in the Leptopodomorpha.
COMMENTS ON COMPONENT‐COMPATIBILITY IN HISTORICAL BIOGEOGRAPHY
- Environmental Science
This paper is a commentary on Zandee and Roos’ (1987; see also Humphries et al., 1988) recent attempt to develop quantitative methods of analysis for cladistic biogeography. Although I share their…
Choosing Among Multiple Equally Parsimonious Cladograms
The issue of choice among multiple equally parsimonious cladograms, and three statistics considered, are addressed: the consistency index, F-ratio, D and the D measure, an application of the Shannon entropy statistic from Gatlin (1972).
Cladistic Analysis and Synthesis: Principles and Definitions, with a Historical Note on Adanson's Familles Des Plantes (1763–1764)
Methods for Investigating Taxonomie Congruence and their Application to the Leptopodomorpha