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Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part III: Algorithm for first approximation

https://doi.org/10.1101/023614
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What this work says

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

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BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
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A Large Version of the Small Parsimony Problem
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
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Evolutionary trees from DNA sequences: A maximum likelihood approach
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An evolutionary model for maximum likelihood alignment of DNA sequences
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Maximum likelihood alignment of DNA sequences
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Characterization of pairwise and multiple sequence alignment errors
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/10.1038/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/10.1073/pnas.0330964100openalex-snapshot
Majority of divergence between closely related DNA samples is due to indels
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/cmb.2007.a006openalex-snapshot
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem
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/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/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/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/msp174openalex-snapshot
Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0
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/sysbio/26.1.77openalex-snapshot
Phylogenetic Analysis Under Dollo's Law
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/10.1101/023622openalex-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.6725608openalex-snapshot
Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
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/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/10.1186/1471-2148-7-40openalex-snapshot
Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
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/10.1101/023598openalex-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/10.1101/023622openalex-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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