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Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis

https://doi.org/10.1101/023598
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Empirical and Structural Models for Insertions and Deletions in the Divergent Evolution of Proteins
inferredcites →https://doi.org/10.1007/3-540-44696-6_1openalex-snapshot
An Improved Model for Statistical Alignment
inferredcites →https://doi.org/10.1007/bf00163848openalex-snapshot
Inching toward reality: An improved likelihood model of sequence evolution
inferredcites →https://doi.org/10.1007/bf00164032openalex-snapshot
The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment
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/s11538-013-9906-6openalex-snapshot
A Note on Probabilistic Models over Strings: The Linear Algebra Approach
inferredcites →https://doi.org/10.1016/0022-2836(86)90289-5openalex-snapshot
Maximum likelihood alignment of DNA sequences
inferredcites →https://doi.org/10.1016/0029-5582(61)90469-2openalex-snapshot
Partial-symmetries of weak interactions
inferredcites →https://doi.org/10.1016/0370-1573(74)90014-3openalex-snapshot
Asymptotic freedom: An approach to strong interactions
inferredcites →https://doi.org/10.1016/j.gene.2008.05.016openalex-snapshot
Characterization of pairwise and multiple sequence alignment errors
inferredcites →https://doi.org/10.1016/j.jmb.2003.08.015openalex-snapshot
Sequence Alignments and Pair Hidden Markov Models Using Evolutionary History
inferredcites →https://doi.org/10.1016/j.jmb.2004.05.045openalex-snapshot
Empirical Analysis of Protein Insertions and Deletions Determining Parameters for the Correct Placement of Gaps in Protein Sequence Alignments
inferredcites →https://doi.org/10.1017/cbo9780511574931openalex-snapshot
Algorithms on Strings, Trees and Sequences
inferredcites →https://doi.org/10.1017/cbo9780511790492openalex-snapshot
Biological Sequence Analysis
inferredcites →https://doi.org/10.1021/j100540a008openalex-snapshot
Exact stochastic simulation of coupled chemical reactions
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/10.1063/1.3062610openalex-snapshot
The Principles of Quantum Mechanics
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.0409137102openalex-snapshot
An algorithm for progressive multiple alignment of sequences with insertions
inferredcites →https://doi.org/10.1073/pnas.1220450110openalex-snapshot
Evolutionary inference via the Poisson Indel Process
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/10.1080/10635150590947041openalex-snapshot
Joint Bayesian Estimation of Alignment and Phylogeny
inferredcites →https://doi.org/10.1089/106652703322756122openalex-snapshot
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees
inferredcites →https://doi.org/10.1089/cmb.2007.a006openalex-snapshot
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem
inferredcites →https://doi.org/10.1090/s0002-9947-1940-0002697-3openalex-snapshot
On the integro-differential equations of purely discontinuous Markoff processes
inferredcites →https://doi.org/10.1093/acprof:oso/9780198567028.001.0001openalex-snapshot
Computational Molecular Evolution
inferredcites →https://doi.org/10.1093/bioinformatics/17.9.803openalex-snapshot
Evolutionary HMMs: a Bayesian approach to multiple alignment
inferredcites →https://doi.org/10.1093/bioinformatics/btg026openalex-snapshot
Statistical alignment based on fragment insertion and deletion models
inferredcites →https://doi.org/10.1093/bioinformatics/btg1019openalex-snapshot
Using guide trees to construct multiple-sequence evolutionary HMMs
inferredcites →https://doi.org/10.1093/bioinformatics/bti1200openalex-snapshot
DNA assembly with gaps (Dawg): simulating sequence evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btl175openalex-snapshot
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny
inferredcites →https://doi.org/10.1093/bioinformatics/btl578openalex-snapshot
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
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/bioinformatics/btn457openalex-snapshot
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees
inferredcites →https://doi.org/10.1093/bioinformatics/btp600openalex-snapshot
Ancestors 1.0: a web server for ancestral sequence reconstruction
inferredcites →https://doi.org/10.1093/bioinformatics/bts198openalex-snapshot
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
inferredcites →https://doi.org/10.1093/dnares/dsl012openalex-snapshot
Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice
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/msp098openalex-snapshot
INDELible: A Flexible Simulator of Biological Sequence Evolution
inferredcites →https://doi.org/10.1093/molbev/msp174openalex-snapshot
Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0
inferredcites →https://doi.org/10.1093/molbev/msp314openalex-snapshot
Timing of Replication Is a Determinant of Neutral Substitution Rates but Does Not Explain Slow Y Chromosome Evolution in Rodents
inferredcites →https://doi.org/10.1093/nar/gkg745openalex-snapshot
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
inferredcites →https://doi.org/10.1093/oso/9780198566106.001.0001openalex-snapshot
Mathematics of Evolution and Phylogeny
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003827openalex-snapshot
Models of Sequence Evolution for DNA Sequences Containing Gaps
inferredcites →https://doi.org/10.1093/sysbio/26.1.77openalex-snapshot
Phylogenetic Analysis Under Dollo's Law
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/10.1101/023622openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations
inferredcites →https://doi.org/10.1101/gr.076521.108openalex-snapshot
Genome-wide nucleotide-level mammalian ancestor reconstruction
inferredcites →https://doi.org/10.1101/gr.098947.109openalex-snapshot
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
inferredcites →https://doi.org/10.1101/gr.2821705openalex-snapshot
ProbCons: Probabilistic consistency-based multiple sequence alignment
inferredcites →https://doi.org/10.1101/gr.6725608openalex-snapshot
Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
inferredcites →https://doi.org/10.1103/physrevd.8.3633openalex-snapshot
Asymptotically Free Gauge Theories. I
inferredcites →https://doi.org/10.1103/physrevlett.19.1264openalex-snapshot
A Model of Leptons
inferredcites →https://doi.org/10.1126/science.1158395openalex-snapshot
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
inferredcites →https://doi.org/10.1126/science.1604319openalex-snapshot
Exhaustive Matching of the Entire Protein Sequence Database
inferredcites →https://doi.org/10.1142/9789812795915_0034openalex-snapshot
Weak and electromagnetic interactions
inferredcites →https://doi.org/10.1142/9789814447362_0019openalex-snapshot
AN ALGORITHM FOR STATISTICAL ALIGNMENT OF SEQUENCES RELATED BY A BINARY TREE
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/10.1186/1471-2105-6-83openalex-snapshot
Bayesian coestimation of phylogeny and sequence alignment
inferredcites →https://doi.org/10.1186/1471-2105-9-137openalex-snapshot
How reliably can we predict the reliability of protein structure predictions?
inferredcites →https://doi.org/10.1186/1471-2148-7-40openalex-snapshot
Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
inferredcites →https://doi.org/10.1186/1755-8417-1-4openalex-snapshot
Mechanisms for human genomic rearrangements
inferredcites →https://doi.org/10.1186/s12859-015-0516-1openalex-snapshot
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
inferredcites →https://doi.org/10.1371/journal.pcbi.0030123openalex-snapshot
Recent Evolutions of Multiple Sequence Alignment Algorithms
inferredcites →https://doi.org/10.1371/journal.pcbi.1000172openalex-snapshot
Probabilistic Phylogenetic Inference with Insertions and Deletions
inferredcites →https://doi.org/10.1371/journal.pone.0034572openalex-snapshot
Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics
inferredcites →https://doi.org/10.2174/138920207783406479openalex-snapshot
Patterns of Insertion and Deletion in Mammalian Genomes

What points at this work

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

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/10.1101/023622openalex-snapshot
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations
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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