Hitch-hiking: a parallel heuristic search strategy, applied to the phylogeny problem

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
M A Charleston

Abstract

The article introduces a parallel heuristic search strategy ("Hitch-hiking") which can be used in conjunction with other random-walk heuristic search strategies. It is applied to an artificial phylogeny problem, in which character sequences are evolved using pseudo-random numbers from a hypothetical ancestral sequence. The objective function to be minimized is the minimum number of character-state changes required on a binary tree that could account for the sequences observed at the tips (leaves) of the tree -- the Maximum Parsimony criterion. The Hitch-hiking strategy is shown to be useful in that it is robust and that on average the solutions found using the strategy are better than those found without. Also the strategy can dynamically provide information on the characteristics of the landscape of the problem. I argue that Hitch-hiking as a scheme for parallelization of existing heuristic search strategies is of potentially very general use, in many areas of combinatorial optimization.

References

Jan 20, 1967·Science·W M Fitch, E Margoliash
Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A Charleston
Apr 1, 1997·Molecular Phylogenetics and Evolution·R D Page, M A Charleston

❮ Previous
Next ❯

Citations

Feb 14, 2002·International Journal for Parasitology·Yannick OutremanFrank Cézilly
Apr 12, 2005·BMC Bioinformatics·Le Sy Vinh, Arndt von Haeseler
Jul 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alan R Lemmon, Michel C Milinkovitch

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

International Journal for Parasitology
Frederic Thomas, Simone Helluy
International Journal for Parasitology
K N Mouritsen
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Miklós Csurös
© 2021 Meta ULC. All rights reserved