Cargando…

Placing Ancient DNA Sequences into Reference Phylogenies

Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the...

Descripción completa

Detalles Bibliográficos
Autores principales:	Martiniano, Rui, De Sanctis, Bianca, Hallast, Pille, Durbin, Richard
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2022
Materias:	Methods
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8857924/ https://www.ncbi.nlm.nih.gov/pubmed/35084493 http://dx.doi.org/10.1093/molbev/msac017

Ejemplares similares

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
por: Martiniano, Rui, et al.
Publicado: (2020)

Selective enrichment of damaged DNA molecules for ancient genome sequencing
por: Gansauge, Marie-Theres, et al.
Publicado: (2014)

Computational challenges in the analysis of ancient DNA
por: Prüfer, Kay, et al.
Publicado: (2010)

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth
por: Glocke, Isabelle, et al.
Publicado: (2017)

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
por: Dolle, Dirk D., et al.
Publicado: (2017)

Contamination detection in sequencing studies using the mitochondrial phylogeny
por: Weissensteiner, Hansi, et al.
Publicado: (2021)

Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal
por: Hallast, Pille, et al.
Publicado: (2016)

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data
por: Kang, Senbai, et al.
Publicado: (2022)

Human auditory ossicles as an alternative optimal source of ancient DNA
por: Sirak, Kendra, et al.
Publicado: (2020)

A minimally destructive protocol for DNA extraction from ancient teeth
por: Harney, Éadaoin, et al.
Publicado: (2021)

Estimating Temporally Variable Selection Intensity from Ancient DNA Data
por: He, Zhangyi, et al.
Publicado: (2023)

Density separation of petrous bone powders for optimized ancient DNA yields
por: Fernandes, Daniel M., et al.
Publicado: (2023)

Efficient detection and assembly of non-reference DNA sequences with synthetic long reads
por: Meleshko, Dmitry, et al.
Publicado: (2022)

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies
por: Yuan, Ke, et al.
Publicado: (2015)

The Effect of Nonreversibility on Inferring Rooted Phylogenies
por: Cherlin, Svetlana, et al.
Publicado: (2018)

Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
por: Rohland, Nadin, et al.
Publicado: (2022)

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease
por: Lees-Miller, James P., et al.
Publicado: (2020)

Log Transformation Improves Dating of Phylogenies
por: Mai, Uyen, et al.
Publicado: (2020)

RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes
por: Nip, Ka Ming, et al.
Publicado: (2020)

The Sequence Ontology: a tool for the unification of genome annotations
por: Eilbeck, Karen, et al.
Publicado: (2005)

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
por: Kozlov, Alexey, et al.
Publicado: (2022)

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)
por: Gillett, Conrad P.D.T., et al.
Publicado: (2014)

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
por: Briggs, Adrian W., et al.
Publicado: (2010)

Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples
por: Bokelmann, Lukas, et al.
Publicado: (2020)

RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
por: de la Rubia, Ivan, et al.
Publicado: (2022)

The Nubeam reference-free approach to analyze metagenomic sequencing reads
por: Dai, Hang, et al.
Publicado: (2020)

PHACT: Phylogeny-Aware Computing of Tolerance for Missense Mutations
por: Kuru, Nurdan, et al.
Publicado: (2022)

Single-cell mutational profiling and clonal phylogeny in cancer
por: Potter, Nicola E., et al.
Publicado: (2013)

Ultra-large alignments using phylogeny-aware profiles
por: Nguyen, Nam-phuong D., et al.
Publicado: (2015)

Phylogeny Estimation by Integration over Isolation with Migration Models
por: Hey, Jody, et al.
Publicado: (2018)

Controls for Phylogeny and Robust Analysis in Pareto Task Inference
por: Adler, Miri, et al.
Publicado: (2021)

ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning
por: Ruiz-Reche, Angel, et al.
Publicado: (2019)

Detection and analysis of ancient segmental duplications in mammalian genomes
por: Pu, Lianrong, et al.
Publicado: (2018)

Detection of simple and complex de novo mutations with multiple reference sequences
por: Garimella, Kiran V., et al.
Publicado: (2020)

PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
por: Malikic, Salem, et al.
Publicado: (2019)

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
por: Zafar, Hamim, et al.
Publicado: (2019)

Ultrafast genome-wide inference of pairwise coalescence times
por: Schweiger, Regev, et al.
Publicado: (2023)

Determining the quality and complexity of next-generation sequencing data without a reference genome
por: Anvar, Seyed Yahya, et al.
Publicado: (2014)

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling
por: Hall, Matthew D, et al.
Publicado: (2019)

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
por: Small, Kerrin S, et al.
Publicado: (2007)

Cannot write session to /tmp/vufind_sessions/sess_3q7nqla98tj4jq6ftp38vajlhf