Fast phylogenetic inference from typing data

Algorithms for Molecular Biology : AMB
João A CarriçoCátia Vaz

Abstract

Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence-based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of sequence and allelic profile data, fast analysis times and their capacity to create common nomenclatures for strains or clones. This led to development of several novel methods and several databases being made available for many microbial species. With the mainstream use of High Throughput Sequencing, the amount of data being accumulated in these databases is huge, storing thousands of different profiles. On the other hand, computing genetic evolutionary distances among a set of typing profiles or taxa dominates the running time of many phylogenetic inference methods. It is important also to note that most of genetic evolution distance definitions rely, even if indirectly, on computing the pairwise Hamming distance among sequences or profiles. We propose here an average-case linear-time algorithm to compute pairwise Hamming distances among a set of taxa under a given Hamming distance threshold. This article includes both a theoretical analysis and extensive experimental results concerning the proposed algorithm. We further ...Continue Reading

References

Jul 1, 1987·Molecular Biology and Evolution·N Saitou, M Nei
Apr 18, 1998·Proceedings of the National Academy of Sciences of the United States of America·M C MaidenB G Spratt
Jan 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·E J FeilB G Spratt
Dec 19, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Richard Desper, Olivier Gascuel
May 20, 2009·BMC Bioinformatics·Alexandre P FranciscoJoão A Carriço
Dec 15, 2010·BMC Bioinformatics·Keith A Jolley, Martin C J Maiden
Mar 30, 2012·Nature Reviews. Genetics·Ziheng Yang, Bruce Rannala
May 10, 2012·BMC Bioinformatics·Alexandre P FranciscoJoäo A Carriço
May 7, 2013·Nature Genetics·Nicholas J CroucherMarc Lipsitch
Feb 11, 2014·Nature Genetics·Claire ChewapreechaStephen D Bentley
Mar 25, 2014·Algorithms for Molecular Biology : AMB·Carl BartonSolon P Pissis
May 1, 2016·Nucleic Acids Research·Bruno Ribeiro-GonçalvesJoão André Carriço
Mar 30, 2017·Microbial Genomics·Andrew J PageSimon R Harris

❮ Previous
Next ❯

Citations

Aug 1, 2020·Briefings in Bioinformatics·Cátia VazAlexandre P Francisco

❮ Previous
Next ❯

Software Mentioned

INNUENDO Platform
wgMLST
Linux
INNUENDO
qsufsort
PHYLOViZ Online
cgMLST
goeBURST
PHYLOViZ
GCC

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.