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Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations

https://doi.org/10.1101/023622
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf00163848openalex-snapshot
Inching toward reality: An improved likelihood model of sequence evolution
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1007/bf02193625openalex-snapshot
An evolutionary model for maximum likelihood alignment of DNA sequences
inferredcites →https://doi.org/10.1007/s002940050130openalex-snapshot
Hairpins create minute inversions in non-coding regions of chloroplast DNA
inferredcites →https://doi.org/10.1016/j.compbiolchem.2010.09.001openalex-snapshot
A stochastic evolution model for residue Insertion–Deletion Independent from Substitution
inferredcites →https://doi.org/10.1016/j.mbs.2013.06.001openalex-snapshot
A new molecular evolution model for limited insertion independent of substitution
inferredcites →https://doi.org/10.1016/j.pbi.2007.02.001openalex-snapshot
Transposable elements and the plant pan-genomes
inferredcites →https://doi.org/10.1016/j.tig.2013.07.002openalex-snapshot
The role of gene conversion in preserving rearrangement hotspots in the human genome
inferredcites →https://doi.org/10.1016/j.ympev.2012.09.015openalex-snapshot
The PNarec method for detection of ancient recombinations through phylogenetic network analysis
inferredcites →https://doi.org/10.1038/nature02564openalex-snapshot
DNA sequence and comparative analysis of chimpanzee chromosome 22
inferredcites →https://doi.org/10.1038/nature04072openalex-snapshot
Initial sequence of the chimpanzee genome and comparison with the human genome
inferredcites →https://doi.org/10.1038/nature07175openalex-snapshot
Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
inferredcites →https://doi.org/10.1038/nrg1348openalex-snapshot
Microsatellites: simple sequences with complex evolution
inferredcites →https://doi.org/10.1038/nrg1895openalex-snapshot
Primate segmental duplications: crucibles of evolution, diversity and disease
inferredcites →https://doi.org/10.1038/nrg2193openalex-snapshot
Gene conversion: mechanisms, evolution and human disease
inferredcites →https://doi.org/10.1073/pnas.0330964100openalex-snapshot
Majority of divergence between closely related DNA samples is due to indels
inferredcites →https://doi.org/10.1073/pnas.0914454107openalex-snapshot
A time-invariant principle of genome evolution
inferredcites →https://doi.org/10.1073/pnas.172510699openalex-snapshot
Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels
inferredcites →https://doi.org/10.1073/pnas.1932072100openalex-snapshot
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
inferredcites →https://doi.org/10.1086/317583openalex-snapshot
Microstructural Changes in Noncoding Chloroplast DNA: Interpretation, Evolution, and Utility of Indels and Inversions in Basal Angiosperm Phylogenetic Inference
inferredcites →https://doi.org/10.1093/acprof:oso/9780198567028.001.0001openalex-snapshot
Computational Molecular Evolution
inferredcites →https://doi.org/10.1093/bioinformatics/bth901openalex-snapshot
A nucleotide substitution model with nearest-neighbour interactions
inferredcites →https://doi.org/10.1093/bioinformatics/bti1200openalex-snapshot
DNA assembly with gaps (Dawg): simulating sequence evolution
inferredcites →https://doi.org/10.1093/bioinformatics/bti376openalex-snapshot
Identification and measurement of neighbor-dependent nucleotide substitution processes
inferredcites →https://doi.org/10.1093/bioinformatics/btm185openalex-snapshot
Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btm402openalex-snapshot
Transducers: an emerging probabilistic framework for modeling indels on trees
inferredcites →https://doi.org/10.1093/gbe/evr074openalex-snapshot
Evolutionary Patterns of Recently Emerged Animal Duplogs
inferredcites →https://doi.org/10.1093/gbe/evv005openalex-snapshot
Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates
inferredcites →https://doi.org/10.1093/molbev/msh043openalex-snapshot
A "Long Indel" Model For Evolutionary Sequence Alignment
inferredcites →https://doi.org/10.1093/molbev/msn275openalex-snapshot
Problems and Solutions for Estimating Indel Rates and Length Distributions
inferredcites →https://doi.org/10.1093/molbev/msq109openalex-snapshot
Evolutionary Pattern of Gene Homogenization between Primate-Specific Paralogs after Human and Macaque Speciation Using the 4-2-4 Method
inferredcites →https://doi.org/10.1093/oso/9780198566106.001.0001openalex-snapshot
Mathematics of Evolution and Phylogeny
inferredcites →https://doi.org/10.1093/sysbio/26.1.77openalex-snapshot
Phylogenetic Analysis Under Dollo's Law
inferredcites →https://doi.org/10.1099/mic.0.28647-0openalex-snapshot
Dispensable genes and foreign DNA in Streptococcus mutans
inferredcites →https://doi.org/10.1101/023598openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis
inferredcites →https://doi.org/10.1101/023606openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part II: Perturbation analyses
inferredcites →https://doi.org/10.1101/023614openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part III: Algorithm for first approximation
inferredcites →https://doi.org/10.1101/gr.076554.108openalex-snapshot
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
inferredcites →https://doi.org/10.1142/s0219720006002168openalex-snapshot
ON THE INFERENCE OF PARSIMONIOUS INDEL EVOLUTIONARY SCENARIOS
inferredcites →https://doi.org/10.1177/0962280208099500openalex-snapshot
Stochastic models of sequence evolution including insertion—deletion events
inferredcites →https://doi.org/10.1186/1471-2105-6-63openalex-snapshot
Evolutionary models for insertions and deletions in a probabilistic modeling framework
inferredcites →https://doi.org/10.1186/1471-2156-14-37openalex-snapshot
Detecting negative selection on recurrent mutations using gene genealogy
inferredcites →https://doi.org/10.1186/1755-8417-1-4openalex-snapshot
Mechanisms for human genomic rearrangements
inferredcites →https://doi.org/10.1371/journal.pcbi.1000172openalex-snapshot
Probabilistic Phylogenetic Inference with Insertions and Deletions
inferredcites →https://doi.org/10.1534/genetics.103.022665openalex-snapshot
Microsatellite Mutation Models
inferredcites →https://doi.org/10.1534/genetics.111.135343openalex-snapshot
The Coalescent with Selection on Copy Number Variants

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00138-xopenalex-snapshot
Genome Alignment
inferred← citeshttps://doi.org/10.1101/023598openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis
inferred← citeshttps://doi.org/10.1101/023606openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part II: Perturbation analyses
inferred← citeshttps://doi.org/10.1101/023614openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part III: Algorithm for first approximation
inferred← citeshttps://doi.org/10.1186/s12859-016-0945-5openalex-snapshot
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map
inferred← citeshttps://doi.org/10.1186/s12859-016-1105-7openalex-snapshot
General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?
inferred← citeshttps://doi.org/10.1186/s12859-016-1167-6openalex-snapshot
General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation
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