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Alignment Uncertainty and Genomic Analysis

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What this work says

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

inferredcites →https://doi.org/10.1006/jmbi.2000.4042openalex-snapshot

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton

inferredcites →https://doi.org/10.1007/bf02193625openalex-snapshot

An evolutionary model for maximum likelihood alignment of DNA sequences

inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot

Comparison of phylogenetic trees

inferredcites →https://doi.org/10.1016/s0378-1119(98)00097-3openalex-snapshot

Multiple sequence alignment with the divide-and-conquer method

inferredcites →https://doi.org/10.1038/nature01644openalex-snapshot

Sequencing and comparison of yeast species to identify genes and regulatory elements

inferredcites →https://doi.org/10.1073/pnas.2036252100openalex-snapshot

Recursions for statistical multiple alignment

inferredcites →https://doi.org/10.1080/106351500750049743openalex-snapshot

Integrating Ambiguously Aligned Regions of DNA Sequences in Phylogenetic Analyses Without Violating Positional Homology

inferredcites →https://doi.org/10.1080/10635150590947041openalex-snapshot

Joint Bayesian Estimation of Alignment and Phylogeny

inferredcites →https://doi.org/10.1093/bioinformatics/15.3.211openalex-snapshot

DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.

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/btl175openalex-snapshot

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

inferredcites →https://doi.org/10.1093/genetics/155.1.431openalex-snapshot

Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites

inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025779openalex-snapshot

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026285openalex-snapshot

Effects of Sequence Alignment and Structural Domains of Ribosomal DNA on Phylogeny Reconstruction for the Protozoan Family Sarcocystidae

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040654openalex-snapshot

The order of sequence alignment can bias the selection of tree topology.

inferredcites →https://doi.org/10.1093/sysbio/43.2.174openalex-snapshot

Evaluating the Phylogenetic Utility of Genes: A Search for Genes Informative About Deep Divergences among Vertebrates

inferredcites →https://doi.org/10.1101/gr.182901openalex-snapshot

Surveying Saccharomyces Genomes to Identify Functional Elements by Comparative DNA Sequence Analysis

inferredcites →https://doi.org/10.1101/gr.2821705openalex-snapshot

ProbCons: Probabilistic consistency-based multiple sequence alignment

inferredcites →https://doi.org/10.1126/science.1084337openalex-snapshot

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

inferredcites →https://doi.org/10.1126/science.1088821openalex-snapshot

Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios

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/10.2307/2413460openalex-snapshot

Evaluating the Phylogenetic Utility of Genes: A Search for Genes Informative About Deep Divergences Among Vertebrates

What points at this work

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

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Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria

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Pitfalls in supermatrix phylogenomics

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Methodologies for Phylogenetic Inference

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Towards Automated Phylogenomic Inference

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Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif‐based sequence alignment amid low genetic distances

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Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families

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In silico analysis of missense substitutions using sequence-alignment based methods

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Phylogenetic diversification of the globin gene superfamily in chordates

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The interface of protein structure, protein biophysics, and molecular evolution

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Revisiting Evaluation of Multiple Sequence Alignment Methods

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Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods

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Applying the Classic Test dN/dS to Detect Selection in Archaea

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Frontiers of statistical decision making and Bayesian analysis : in honor of James O. Berger

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Error Detection and Correction of Gene Trees

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RNA Secondary Structure Prediction from Multi-Aligned Sequences

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Inferring Trees

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Enhancing Statistical Multiple Sequence Alignment and Tree Inference Using Structural Information

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Detection and Quantitative Assessment of Horizontal Gene Transfer

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Evolution of cis-Regulatory Sequences in Drosophila

inferred← citeshttps://doi.org/10.1007/978-1-62703-646-7_13openalex-snapshot

PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences

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Bioinformatics and Translation Initiation

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Bioinformatics and Translation Elongation

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Protein Isoelectric Point and Helicobacter pylori

inferred← citeshttps://doi.org/10.1007/978-3-032-26891-4_17openalex-snapshot

FIREFLY: PHYlogeny-Informed REpresentation Learning to Estimate PHyLogenetic dIstances

inferred← citeshttps://doi.org/10.1007/978-3-319-05269-4_27openalex-snapshot

Bayesian Multiple Protein Structure Alignment

inferred← citeshttps://doi.org/10.1007/978-3-319-07953-0_20openalex-snapshot

RRCA: Ultra-Fast Multiple In-species Genome Alignments

inferred← citeshttps://doi.org/10.1007/978-3-319-54064-1_6openalex-snapshot

Alignment and Mapping

inferred← citeshttps://doi.org/10.1007/978-3-319-90684-3_12openalex-snapshot

Nucleotide Substitution Models and Evolutionary Distances

inferred← citeshttps://doi.org/10.1007/978-3-319-90684-3_15openalex-snapshot

Distance-Based Phylogenetic Methods

inferred← citeshttps://doi.org/10.1007/978-3-319-90684-3_19openalex-snapshot

Fundamentals of Proteomics

inferred← citeshttps://doi.org/10.1007/978-3-642-00952-5_13openalex-snapshot

Large-Scale Analyses of Positive Selection Using Codon Models

inferred← citeshttps://doi.org/10.1007/978-3-642-12683-3_9openalex-snapshot

Alignment-Free Phylogenetic Reconstruction

inferred← citeshttps://doi.org/10.1007/978-3-642-20036-6_14openalex-snapshot

PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling

inferred← citeshttps://doi.org/10.1007/978-3-642-38036-5_26openalex-snapshot

Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication

inferred← citeshttps://doi.org/10.1007/978-3-642-40453-5_20openalex-snapshot

MSARC: Multiple Sequence Alignment by Residue Clustering

inferred← citeshttps://doi.org/10.1007/978-981-95-2550-8_5openalex-snapshot

On the Wald Space for Phylogenetic Trees

inferred← citeshttps://doi.org/10.1007/s00239-011-9461-4openalex-snapshot

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

inferred← citeshttps://doi.org/10.1007/s00239-011-9463-2openalex-snapshot

Selection-Driven Divergence After Gene Duplication in Arabidopsis thaliana

inferred← citeshttps://doi.org/10.1007/s00251-008-0304-4openalex-snapshot

Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes

inferred← citeshttps://doi.org/10.1007/s10529-022-03277-4openalex-snapshot

Molecular cloning and characterization of an alpha-amylase inhibitor (TkAAI) gene from Trichosanthes kirilowii Maxim.

inferred← citeshttps://doi.org/10.1007/s10539-026-10027-7openalex-snapshot

Defining biological species with alternational DNA sequence assertions: a practicum

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Decision-Tree-based data mining and rule induction for predicting and mapping soil bacterial diversity

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Scalable alignment-free feature extraction approach for genome data and their cluster analysis

inferred← citeshttps://doi.org/10.1007/s11538-013-9906-6openalex-snapshot

A Note on Probabilistic Models over Strings: The Linear Algebra Approach

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Ultrastructural and immunocytochemical investigation of paramylon combined with new 18S rDNA-based secondary structure analysis clarifies phylogenetic affiliation of Entosiphon sulcatum (Euglenida: Euglenozoa)

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Tree Evaluation and Robustness Testing

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Tree Evaluation and Robustness Testing

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Phylogenomic analysis and the origin and early evolution of viruses

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Population Genomic and Phylogenomic Insights into the Evolution of Physiology and Behaviour in Social Insects

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The type V effectors for CRISPR/Cas-mediated genome engineering in plants

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Sensitivity of sequence methods in the study of neighborhood change in the United States

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Functional and Structural Basis for a Bacteriophage Homolog of Human RAD52

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Complete chloroplast genome data for Mimosa diplotricha and Mimosa diplotricha var. inermis from China

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Complete chloroplast genome data of Ranunculus membranaceus (Ranunculaceae), an important medicinal plant species

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Bioinformatics predicts diverse Aspergillus hydrophobins with novel properties

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Comparative genomics of gene regulation—conservation and divergence of cis-regulatory information

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Characterization of pairwise and multiple sequence alignment errors

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Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes

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PEER: A direct method for biosequence pattern mining through waits of optimal k-mers

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Coevolution Predicts Direct Interactions between mtDNA-Encoded and nDNA-Encoded Subunits of Oxidative Phosphorylation Complex I

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A new cloning system using a mutant esterase containing MCS as an indicator for gene cloning

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Global alignment of molecular sequences via ancestral state reconstruction

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Transcription factor binding variation in the evolution of gene regulation

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The ecology of horizontal gene transfer

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Genomes as documents of evolutionary history

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Three roads diverged? Routes to phylogeographic inference

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An Integrated Perspective on Phylogenetic Workflows

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Evolution of DUF1313 family members across plant species and their association with maize photoperiod sensitivity

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Towards the phylogeny of chafers (Sericini): Analysis of alignment-variable sequences and the evolution of segment numbers in the antennal club

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Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson

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Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationship of pigeons within Neoaves

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Can sensitivity analysis help to detect long-branch attraction?

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Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping

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Beyond phylogeny: pelecaniform and ciconiiform birds, and long-term niche stability

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Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster

inferred← citeshttps://doi.org/10.1016/j.ympev.2015.04.008openalex-snapshot

Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles

inferred← citeshttps://doi.org/10.1016/j.ympev.2015.05.011openalex-snapshot

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

inferred← citeshttps://doi.org/10.1016/j.ympev.2015.12.011openalex-snapshot

Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation

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Virus classification in 60-dimensional protein space

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Biases of tree-independent-character-subsampling methods

inferred← citeshttps://doi.org/10.1016/j.ympev.2016.07.001openalex-snapshot

PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences

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Evidence of absence treated as absence of evidence: The effects of variation in the number and distribution of gaps treated as missing data on the results of standard maximum likelihood analysis

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107662openalex-snapshot

KINN: An alignment-free accurate phylogeny reconstruction method based on inner distance distributions of k-mer pairs in biological sequences

inferred← citeshttps://doi.org/10.1017/cbo9781139095112openalex-snapshot

Bayesian Evolutionary Analysis with BEAST

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Bacterial Cells Engineered with Synthetic Genetic Materials for Blind Testing of Random Mutagenesis

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Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics

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Comparative assessment of methods for aligning multiple genome sequences

inferred← citeshttps://doi.org/10.1038/nprot.2011.393openalex-snapshot

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

inferred← citeshttps://doi.org/10.1038/nrg2185openalex-snapshot

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes

inferred← citeshttps://doi.org/10.1038/nrg2327openalex-snapshot

Danger! Uncertain alignments!

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Statistical analysis strategies for association studies involving rare variants

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Phylogenies from unaligned proteomes using sequence environments of amino acid residues

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An intelligent recognition method of chromosome rearrangement patterns based on information entropy

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A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins

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Comparative analysis of whole chloroplast genomes of three common species of Nekemias from vine tea

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Inferring phylogenies of evolving sequences without multiple sequence alignment

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Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

inferred← citeshttps://doi.org/10.1042/bst0370783openalex-snapshot

Evidence for an episodic model of protein sequence evolution

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Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

inferred← citeshttps://doi.org/10.1073/pnas.0806759105openalex-snapshot

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

inferred← citeshttps://doi.org/10.1073/pnas.0905115106openalex-snapshot

Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method

inferred← citeshttps://doi.org/10.1073/pnas.0912949107openalex-snapshot

Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes

inferred← citeshttps://doi.org/10.1073/pnas.1006756107openalex-snapshot

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

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Genes involved in convergent evolution of eusociality in bees

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Evolutionary inference via the Poisson Indel Process

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The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa

inferred← citeshttps://doi.org/10.1080/07391102.2013.770371openalex-snapshot

Identifying subset errors in multiple sequence alignments

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Intelligent mining of large-scale bio-data: Bioinformatics applications

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The transformation of school culture and teachers’ perspectives on SEND within Guyana’s mainstream elementary school system between the decade 2014 and 2024.

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Sequences and transcriptional analysis ofCoffea arabicavar. Caturra andCoffea libericaplant responses to coffee berry borerHypothenemus hampei(Coleoptera: Curculionidae: Scolytinae) attack

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Phylogenomics of tomato chloroplasts using assembly and alignment-free method

inferred← citeshttps://doi.org/10.1088/1742-5468/2009/12/p12010openalex-snapshot

Clustering with shallow trees

inferred← citeshttps://doi.org/10.1089/cmb.2010.0325openalex-snapshot

Tracing the Most Parsimonious Indel History

inferred← citeshttps://doi.org/10.1089/cmb.2018.0239openalex-snapshot

Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.001.0001openalex-snapshot

Animal Evolution

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0003openalex-snapshot

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0004openalex-snapshot

Foreword

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0007openalex-snapshot

Contributors

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.002.0008openalex-snapshot

Introduction

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0001openalex-snapshot

The earliest fossil record of the animals and its significance

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0002openalex-snapshot

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0003openalex-snapshot

Genomic, phylogenetic, and cell biological insights into metazoan origins

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0004openalex-snapshot

The mouth, the anus, and the blastopore—open questions about questionable openings

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0005openalex-snapshot

Origins of metazoan body plans: the larval revolution

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0006openalex-snapshot

Assembling the spiralian tree of life

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0007openalex-snapshot

The evolution of nervous system centralization

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0008openalex-snapshot

The origins and evolution of the Ecdysozoa

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0009openalex-snapshot

Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0010openalex-snapshot

Molecular genetic insights into deuterostome evolution from the direct-developing hemichordateSaccoglossus kowalevskii

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0011openalex-snapshot

Invertebrate Problematica: kinds, causes, and solutions

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0012openalex-snapshot

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0013openalex-snapshot

Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0014openalex-snapshot

The animal in the genome: comparative genomics and evolution

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0015openalex-snapshot

MicroRNAs and metazoan phylogeny: big trees from little genes

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0016openalex-snapshot

The evolution of developmental gene networks: lessons from comparative studies on holometabolous insects

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0017openalex-snapshot

Conserved developmental processes and the evolution of novel traits: wounds, embryos, veins, and butterfly eyespots

inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199549429.003.0018openalex-snapshot

Reassembling animal evolution: a four-dimensional puzzle

inferred← citeshttps://doi.org/10.1093/bib/bbn013openalex-snapshot

Recent developments in the MAFFT multiple sequence alignment program

inferred← citeshttps://doi.org/10.1093/bib/bbt038openalex-snapshot

Fighting against uncertainty: an essential issue in bioinformatics

inferred← citeshttps://doi.org/10.1093/bioinformatics/btad630openalex-snapshot

PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score

inferred← citeshttps://doi.org/10.1093/bioinformatics/btae255openalex-snapshot

A machine-learning-based alternative to phylogenetic bootstrap

inferred← citeshttps://doi.org/10.1093/bioinformatics/btn301openalex-snapshot

Connect the dots: exposing hidden protein family connections from the entire sequence tree

inferred← citeshttps://doi.org/10.1093/bioinformatics/btn457openalex-snapshot

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

inferred← citeshttps://doi.org/10.1093/bioinformatics/btp228openalex-snapshot

Predictions of RNA secondary structure by combining homologous sequence information

inferred← citeshttps://doi.org/10.1093/bioinformatics/btp452openalex-snapshot

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

inferred← citeshttps://doi.org/10.1093/bioinformatics/btp552openalex-snapshot

Reproducing the manual annotation of multiple sequence alignments using a SVM classifier

inferred← citeshttps://doi.org/10.1093/bioinformatics/btp580openalex-snapshot

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

inferred← citeshttps://doi.org/10.1093/bioinformatics/btr553openalex-snapshot

F AST SP: linear time calculation of alignment accuracy

inferred← citeshttps://doi.org/10.1093/bioinformatics/btr587openalex-snapshot

STRIKE: evaluation of protein MSAs using a single 3D structure

inferred← citeshttps://doi.org/10.1093/bioinformatics/btr701openalex-snapshot

Measuring the distance between multiple sequence alignments

inferred← citeshttps://doi.org/10.1093/bioinformatics/btt360openalex-snapshot

Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz082openalex-snapshot

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz236openalex-snapshot

Protein multiple alignments: sequence-based versus structure-based programs

inferred← citeshttps://doi.org/10.1093/g3journal/jkab333openalex-snapshot

Frequent lineage-specific substitution rate changes support an episodic model for protein evolution

inferred← citeshttps://doi.org/10.1093/gbe/evab133openalex-snapshot

Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes

inferred← citeshttps://doi.org/10.1093/gbe/evae183openalex-snapshot

Evolution of Key Oxygen-Sensing Genes Is Associated with Hypoxia Tolerance in Fishes

inferred← citeshttps://doi.org/10.1093/gbe/evp032openalex-snapshot

Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus

inferred← citeshttps://doi.org/10.1093/gbe/evq007openalex-snapshot

Conservation of Human Microsatellites across 450 Million Years of Evolution

inferred← citeshttps://doi.org/10.1093/gbe/evq008openalex-snapshot

Positive Selection Differs between Protein Secondary Structure Elements in Drosophila

inferred← citeshttps://doi.org/10.1093/gbe/evt017openalex-snapshot

Improving Genome-Wide Scans of Positive Selection by Using Protein Isoforms of Similar Length

inferred← citeshttps://doi.org/10.1093/gbe/evv127openalex-snapshot

Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty

inferred← citeshttps://doi.org/10.1093/gbe/evx084openalex-snapshot

Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation

inferred← citeshttps://doi.org/10.1093/gigascience/giad022openalex-snapshot

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

inferred← citeshttps://doi.org/10.1093/jole/lzag001openalex-snapshot

Phylogenetic inference from cognate word forms

inferred← citeshttps://doi.org/10.1093/molbev/msaa114openalex-snapshot

Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

inferred← citeshttps://doi.org/10.1093/molbev/msae109openalex-snapshot

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels

inferred← citeshttps://doi.org/10.1093/molbev/msae177openalex-snapshot

Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications

inferred← citeshttps://doi.org/10.1093/molbev/msaf154openalex-snapshot

Detecting Interspecific Positive Selection Using Convolutional Neural Networks

inferred← citeshttps://doi.org/10.1093/molbev/msag097openalex-snapshot

AliFilter: a machine learning approach to alignment filtering

inferred← citeshttps://doi.org/10.1093/molbev/msag182openalex-snapshot

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

inferred← citeshttps://doi.org/10.1093/molbev/msp105openalex-snapshot

A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies

inferred← citeshttps://doi.org/10.1093/molbev/msp289openalex-snapshot

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1

inferred← citeshttps://doi.org/10.1093/molbev/msp299openalex-snapshot

Multiple Evolutionary Rate Classes in Animal Genome Evolution

inferred← citeshttps://doi.org/10.1093/molbev/msq115openalex-snapshot

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

inferred← citeshttps://doi.org/10.1093/molbev/msq165openalex-snapshot

Different Phylogenomic Approaches to Resolve the Evolutionary Relationships among Model Fish Species

inferred← citeshttps://doi.org/10.1093/molbev/msr177openalex-snapshot

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

inferred← citeshttps://doi.org/10.1093/molbev/msr272openalex-snapshot

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

inferred← citeshttps://doi.org/10.1093/molbev/mss167openalex-snapshot

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

inferred← citeshttps://doi.org/10.1093/molbev/mss256openalex-snapshot

Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis

inferred← citeshttps://doi.org/10.1093/molbev/mst036openalex-snapshot

Prevalence of Multinucleotide Replacements in Evolution of Primates and Drosophila

inferred← citeshttps://doi.org/10.1093/molbev/mst062openalex-snapshot

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

inferred← citeshttps://doi.org/10.1093/molbev/mst167openalex-snapshot

The Evolution of Small Insertions and Deletions in the Coding Genes of Drosophila melanogaster

inferred← citeshttps://doi.org/10.1093/molbev/msu046openalex-snapshot

Emergence and Evolutionary Analysis of the Human DDR Network: Implications in Comparative Genomics and Downstream Analyses

inferred← citeshttps://doi.org/10.1093/molbev/msu117openalex-snapshot

TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

inferred← citeshttps://doi.org/10.1093/molbev/msu174openalex-snapshot

Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection

inferred← citeshttps://doi.org/10.1093/molbev/msu184openalex-snapshot

Simultaneous Bayesian Estimation of Alignment and Phylogeny under a Joint Model of Protein Sequence and Structure

inferred← citeshttps://doi.org/10.1093/molbev/msz101openalex-snapshot

Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter

inferred← citeshttps://doi.org/10.1093/molbev/msz142openalex-snapshot

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

inferred← citeshttps://doi.org/10.1093/nar/gkq255openalex-snapshot

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences

inferred← citeshttps://doi.org/10.1093/nar/gkq442openalex-snapshot

DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS

inferred← citeshttps://doi.org/10.1093/nar/gkq443openalex-snapshot

GUIDANCE: a web server for assessing alignment confidence scores

inferred← citeshttps://doi.org/10.1093/nar/gkr244openalex-snapshot

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences

inferred← citeshttps://doi.org/10.1093/nar/gkr245openalex-snapshot

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

inferred← citeshttps://doi.org/10.1093/nar/gkr334openalex-snapshot

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

inferred← citeshttps://doi.org/10.1093/nar/gkt003openalex-snapshot

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

inferred← citeshttps://doi.org/10.1093/nar/gkt1138openalex-snapshot

Phylo SI: a new genome-wide approach for prokaryotic phylogeny

inferred← citeshttps://doi.org/10.1093/nar/gkx179openalex-snapshot

PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes

inferred← citeshttps://doi.org/10.1093/nar/gkx704openalex-snapshot

Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts

inferred← citeshttps://doi.org/10.1093/sysbio/syaa054openalex-snapshot

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

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