Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites

In modern phylogenetics, when comparing sequences of DNA the traditional approach assumes that nu- cleotide substitutions follow a Markov model, that sites on a DNA sequence evolve independently and in the same way. However, recent studies have shown that some positions in DNA sequences remain invar...

Descripción completa

Detalles Bibliográficos
Autor: Mañez Fernandez, Davinia
Tipo de recurso: tesis de maestría
Fecha de publicación:2023
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/392846
Acceso en línea:https://hdl.handle.net/2117/392846
Access Level:acceso abierto
Palabra clave:Markov processes
Biomathematics
Phylogenetic tree
Markov process
flattening
invariable parameters
invariable sites
Markov, Processos de
Biomatemàtica
Classificació AMS::92 Biology and other natural sciences
Àrees temàtiques de la UPC::Matemàtiques i estadística
id ES_f29c308fed42e836df65ac26d63b2f56
oai_identifier_str oai:upcommons.upc.edu:2117/392846
network_acronym_str ES
network_name_str España
repository_id_str
spelling Algebraic statistics in phylogenetic reconstruction: incorporating invariable sitesMañez Fernandez, DaviniaMarkov processesBiomathematicsPhylogenetic treeMarkov processflatteninginvariable parametersinvariable sitesMarkov, Processos deBiomatemàticaClassificació AMS::92 Biology and other natural sciencesÀrees temàtiques de la UPC::Matemàtiques i estadísticaIn modern phylogenetics, when comparing sequences of DNA the traditional approach assumes that nu- cleotide substitutions follow a Markov model, that sites on a DNA sequence evolve independently and in the same way. However, recent studies have shown that some positions in DNA sequences remain invariant. This thesis aims to investigate cases where certain regions of DNA sequences do not change throughout the evolutionary process. The approach, inspired by the work of Allman and Rhodes in [1], considers a model where a proportion of sites in the DNA sequences cannot vary, while the remaining sites are variable. This model is referred to as the general Markov model plus invariable sites (GM + I ). In [1] they obtain formulae to recover the called invariable parameters involved in the GM + I model. We implement a computational method based on this proposition using Python and evaluate its performance using simulated data. The performance of the method is analyzed in different situations, and potential improvements and variations based on our findings are suggested.Universitat Politècnica de CatalunyaCasanellas Rius, MartaFernández Sánchez, Jesús20232023-06-0120232023-08-28master thesishttp://purl.org/coar/resource_type/c_bdccNAhttp://purl.org/coar/version/c_be7fb7dd8ff6fe43info:eu-repo/semantics/masterThesisapplication/pdfhttps://hdl.handle.net/2117/392846reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3928462026-05-27T15:37:01Z
dc.title.none.fl_str_mv Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
title Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
spellingShingle Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
Mañez Fernandez, Davinia
Markov processes
Biomathematics
Phylogenetic tree
Markov process
flattening
invariable parameters
invariable sites
Markov, Processos de
Biomatemàtica
Classificació AMS::92 Biology and other natural sciences
Àrees temàtiques de la UPC::Matemàtiques i estadística
title_short Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
title_full Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
title_fullStr Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
title_full_unstemmed Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
title_sort Algebraic statistics in phylogenetic reconstruction: incorporating invariable sites
dc.creator.none.fl_str_mv Mañez Fernandez, Davinia
author Mañez Fernandez, Davinia
author_facet Mañez Fernandez, Davinia
author_role author
dc.contributor.none.fl_str_mv Casanellas Rius, Marta
Fernández Sánchez, Jesús
dc.subject.none.fl_str_mv Markov processes
Biomathematics
Phylogenetic tree
Markov process
flattening
invariable parameters
invariable sites
Markov, Processos de
Biomatemàtica
Classificació AMS::92 Biology and other natural sciences
Àrees temàtiques de la UPC::Matemàtiques i estadística
topic Markov processes
Biomathematics
Phylogenetic tree
Markov process
flattening
invariable parameters
invariable sites
Markov, Processos de
Biomatemàtica
Classificació AMS::92 Biology and other natural sciences
Àrees temàtiques de la UPC::Matemàtiques i estadística
description In modern phylogenetics, when comparing sequences of DNA the traditional approach assumes that nu- cleotide substitutions follow a Markov model, that sites on a DNA sequence evolve independently and in the same way. However, recent studies have shown that some positions in DNA sequences remain invariant. This thesis aims to investigate cases where certain regions of DNA sequences do not change throughout the evolutionary process. The approach, inspired by the work of Allman and Rhodes in [1], considers a model where a proportion of sites in the DNA sequences cannot vary, while the remaining sites are variable. This model is referred to as the general Markov model plus invariable sites (GM + I ). In [1] they obtain formulae to recover the called invariable parameters involved in the GM + I model. We implement a computational method based on this proposition using Python and evaluate its performance using simulated data. The performance of the method is analyzed in different situations, and potential improvements and variations based on our findings are suggested.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-06-01
2023
2023-08-28
dc.type.none.fl_str_mv master thesis
http://purl.org/coar/resource_type/c_bdcc
NA
http://purl.org/coar/version/c_be7fb7dd8ff6fe43
dc.type.openaire.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/392846
url https://hdl.handle.net/2117/392846
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universitat Politècnica de Catalunya
publisher.none.fl_str_mv Universitat Politècnica de Catalunya
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869424297649373184
score 15,301603

Similares en LA Referencia