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Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

https://doi.org/10.1093/molbev/msz142
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What this work says

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

inferredcites →https://doi.org/10.1002/prot.20527openalex-snapshot
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
inferredcites →https://doi.org/10.1006/aama.2001.0759openalex-snapshot
Geometry of the Space of Phylogenetic Trees
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/10.1007/0-387-27733-1_14openalex-snapshot
Statistical Alignment: Recent Progress, New Applications, and Challenges
inferredcites →https://doi.org/10.1007/978-1-4939-6622-6_14openalex-snapshot
Inferring Trees
inferredcites →https://doi.org/10.1017/cbo9780511790492openalex-snapshot
Biological Sequence Analysis
inferredcites →https://doi.org/10.1071/sb15001openalex-snapshot
Molecular homology and multiple-sequence alignment: an analysis of concepts and practice
inferredcites →https://doi.org/10.1080/10635150500541730openalex-snapshot
Multiple Sequence Alignment Accuracy and Phylogenetic Inference
inferredcites →https://doi.org/10.1080/10635150600899780openalex-snapshot
Statistical Methods in Molecular Evolution
inferredcites →https://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
inferredcites →https://doi.org/10.1093/bib/bbv099openalex-snapshot
Multiple sequence alignment modeling: methods and applications
inferredcites →https://doi.org/10.1093/bioinformatics/15.1.87openalex-snapshot
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btt636openalex-snapshot
PSAR-Align: improving multiple sequence alignment using probabilistic sampling
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/gbe/evv127openalex-snapshot
Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty
inferredcites →https://doi.org/10.1093/molbev/msm060openalex-snapshot
Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments
inferredcites →https://doi.org/10.1093/molbev/msp098openalex-snapshot
INDELible: A Flexible Simulator of Biological Sequence Evolution
inferredcites →https://doi.org/10.1093/molbev/msq066openalex-snapshot
An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty
inferredcites →https://doi.org/10.1093/molbev/msr272openalex-snapshot
The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/mss256openalex-snapshot
Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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/nar/gkv318openalex-snapshot
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025808openalex-snapshot
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/46.1.69openalex-snapshot
Is the Felsenstein Zone a Fly Trap?
inferredcites →https://doi.org/10.1093/sysbio/syv033openalex-snapshot
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
inferredcites →https://doi.org/10.1093/sysbio/syw074openalex-snapshot
Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking
inferredcites →https://doi.org/10.1101/gr.1960404openalex-snapshot
MAVID: Constrained Ancestral Alignment of Multiple Sequences
inferredcites →https://doi.org/10.1109/tcbb.2010.3openalex-snapshot
A Fast Algorithm for Computing Geodesic Distances in Tree Space
inferredcites →https://doi.org/10.1126/science.1151532openalex-snapshot
Alignment Uncertainty and Genomic Analysis
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.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1371/journal.pone.0030288openalex-snapshot
Accounting For Alignment Uncertainty in Phylogenomics

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The Gluopsins: Opsins without the Retinal Binding Lysine
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443003openalex-snapshot
Additional file 12 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443009openalex-snapshot
Additional file 14 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443018openalex-snapshot
Additional file 16 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443021openalex-snapshot
Additional file 17 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443024openalex-snapshot
Additional file 18 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443030openalex-snapshot
Additional file 2 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443033openalex-snapshot
Additional file 3 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443036openalex-snapshot
Additional file 4 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443039openalex-snapshot
Additional file 5 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443042openalex-snapshot
Additional file 6 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443045openalex-snapshot
Additional file 7 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443048openalex-snapshot
Additional file 8 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443051openalex-snapshot
Additional file 9 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.64898/2025.12.20.694765openalex-snapshot
The phylogenetic context for the origin of a unique purple-green photosymbiosis
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