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PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Resolving Animal Phylogeny: A Sledgehammer for a Tough Nut?
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Perils of Paralogy: Using HSP70 Genes for Inferring Organismal Phylogenies
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Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btr259openalex-snapshot
ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms
inferredcites →https://doi.org/10.1093/bioinformatics/bts006openalex-snapshot
Roundup 2.0: enabling comparative genomics for over 1800 genomes
inferredcites →https://doi.org/10.1093/molbev/msq089openalex-snapshot
Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
inferredcites →https://doi.org/10.1093/molbev/msr185openalex-snapshot
Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
inferredcites →https://doi.org/10.1093/nar/30.7.1575openalex-snapshot
An efficient algorithm for large-scale detection of protein families
inferredcites →https://doi.org/10.1093/nar/gki198openalex-snapshot
MAFFT version 5: improvement in accuracy of multiple sequence alignment
inferredcites →https://doi.org/10.1093/nar/gkp931openalex-snapshot
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
inferredcites →https://doi.org/10.1093/nar/gkr1261openalex-snapshot
Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs
inferredcites →https://doi.org/10.1098/rspb.2009.0896openalex-snapshot
Assessing the root of bilaterian animals with scalable phylogenomic methods
inferredcites →https://doi.org/10.1098/rspb.2012.0744openalex-snapshot
Insect phylogenomics: results, problems and the impact of matrix composition
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1146/annurev-ento-120710-100538openalex-snapshot
Advances in Insect Phylogeny at the Dawn of the Postgenomic Era
inferredcites →https://doi.org/10.1186/1471-2105-12-11openalex-snapshot
OrthoInspector: comprehensive orthology analysis and visual exploration
inferredcites →https://doi.org/10.1186/1471-2148-7-s1-s2openalex-snapshot
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inferredcites →https://doi.org/10.1186/1471-2148-9-157openalex-snapshot
HaMStR: Profile hidden markov model based search for orthologs in ESTs
inferredcites →https://doi.org/10.1186/1741-7007-10-47openalex-snapshot
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi
inferredcites →https://doi.org/10.1186/gb-2008-9-10-235openalex-snapshot
Large-scale assignment of orthology: back to phylogenetics?
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pcbi.1000262openalex-snapshot
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
inferredcites →https://doi.org/10.1371/journal.pone.0000383openalex-snapshot
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
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Broad Phylogenomic Sampling and the Sister Lineage of Land Plants
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The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships
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Ancient paralogy in the cpDNA trnL‐F region in Annonaceae: implications for plant molecular systematics
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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inferred← citeshttps://doi.org/10.1038/s41467-023-36151-6openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41559-017-0331-3openalex-snapshot
Ctenophore relationships and their placement as the sister group to all other animals
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Incongruence in the phylogenomics era
inferred← citeshttps://doi.org/10.1038/s41597-024-03700-7openalex-snapshot
Transcriptome data for an ancient ‘living-fossil’ mollusc, Entemnotrochus rumphii
inferred← citeshttps://doi.org/10.1038/s41598-018-19996-6openalex-snapshot
Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach
inferred← citeshttps://doi.org/10.1038/s41598-019-56728-wopenalex-snapshot
New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships
inferred← citeshttps://doi.org/10.1038/s42003-025-09153-xopenalex-snapshot
Triploidy drives vector capacity and expansion of the parthenogenetic tick Haemaphysalis longicornis
inferred← citeshttps://doi.org/10.1073/pnas.2302361120openalex-snapshot
Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting
inferred← citeshttps://doi.org/10.1080/00222933.2014.963184openalex-snapshot
A review on deep molluscan phylogeny: old markers, integrative approaches, persistent problems
inferred← citeshttps://doi.org/10.1080/14772000.2020.1827077openalex-snapshot
Phylogenomic inference of the interrelationships of Lake Baikal sponges
inferred← citeshttps://doi.org/10.1093/bioadv/vbae189openalex-snapshot
wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btw824openalex-snapshot
phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics
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Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)
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Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata
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Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae
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Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks
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inferred← citeshttps://doi.org/10.1093/nar/gkv487openalex-snapshot
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
inferred← citeshttps://doi.org/10.1093/nar/gkz333openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syab070openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syw099openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/sysbio/syz029openalex-snapshot
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inferred← citeshttps://doi.org/10.1098/rsos.220939openalex-snapshot
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inferred← citeshttps://doi.org/10.1098/rspb.2019.0111openalex-snapshot
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inferred← citeshttps://doi.org/10.1098/rspb.2019.0115openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/170696openalex-snapshot
Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships
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Surprising amount of stasis in repetitive genome content across the Brassicales
inferred← citeshttps://doi.org/10.1101/202119openalex-snapshot
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Contribution of hybridization to the evolution of a derived reproductive strategy in ricefishes
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inferred← citeshttps://doi.org/10.1101/398446openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/1755-0998.12552openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/1755-0998.13072openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/1755-0998.13287openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/1755-0998.13817openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jeb.13439openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jse.12167openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/mec.15339openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/nph.15099openalex-snapshot
Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)
inferred← citeshttps://doi.org/10.1111/syen.12217openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/syen.12406openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/syen.12414openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.12201openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.12208openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.12211openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.12457openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.12676openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.70071openalex-snapshot
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inferred← citeshttps://doi.org/10.1126/sciadv.adx1754openalex-snapshot
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inferred← citeshttps://doi.org/10.1127/pip/2017/0075openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12862-017-0973-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12862-017-1066-0openalex-snapshot
Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)
inferred← citeshttps://doi.org/10.1186/s12862-018-1142-0openalex-snapshot
Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits
inferred← citeshttps://doi.org/10.1186/s12862-019-1370-yopenalex-snapshot
Transcriptomic analysis confirms differences among nuclear genomes of cryptic earthworm lineages living in sympatry
inferred← citeshttps://doi.org/10.1186/s12862-019-1444-xopenalex-snapshot
Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny
inferred← citeshttps://doi.org/10.1186/s12862-021-01772-2openalex-snapshot
Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference
inferred← citeshttps://doi.org/10.1186/s12862-021-01779-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12920-014-0064-yopenalex-snapshot
FLAGS, frequently mutated genes in public exomes
inferred← citeshttps://doi.org/10.1371/journal.pbio.2005359openalex-snapshot
Comparative genomics and the nature of placozoan species
inferred← citeshttps://doi.org/10.1371/journal.pbio.3000255openalex-snapshot
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001827openalex-snapshot
OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002632openalex-snapshot
The promise and pitfalls of synteny in phylogenomics
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002794openalex-snapshot
A taxon-rich and genome-scale phylogeny of Opisthokonta
inferred← citeshttps://doi.org/10.1371/journal.pone.0082615openalex-snapshot
Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study
inferred← citeshttps://doi.org/10.1371/journal.pone.0279091openalex-snapshot
Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus)
inferred← citeshttps://doi.org/10.15252/msb.202110427openalex-snapshot
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
inferred← citeshttps://doi.org/10.1534/g3.115.020164openalex-snapshot
De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
inferred← citeshttps://doi.org/10.1534/g3.117.300233openalex-snapshot
KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences
inferred← citeshttps://doi.org/10.18061/bssb.v3i2.9267openalex-snapshot
A Cnidarian Phylogenomic Tree Fitted With Hundreds of 18S Leaves
inferred← citeshttps://doi.org/10.18516/0026openalex-snapshot
Spider phylogenomics: untangling the Spider Tree of Life
inferred← citeshttps://doi.org/10.24349/pjye-gkeoopenalex-snapshot
Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
inferred← citeshttps://doi.org/10.31390/gradschool_theses.1087openalex-snapshot
Phylogenetic Tree Construction for Starfish and Primate Genomes via Alignment Free Methods
inferred← citeshttps://doi.org/10.32469/10355/91652openalex-snapshot
Genomics of small RNAs in the Brassicales
inferred← citeshttps://doi.org/10.3389/fevo.2021.769565openalex-snapshot
Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes
inferred← citeshttps://doi.org/10.3389/fevo.2024.1243221openalex-snapshot
Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea
inferred← citeshttps://doi.org/10.3389/fgene.2020.598196openalex-snapshot
Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data
inferred← citeshttps://doi.org/10.3389/fphys.2018.01833openalex-snapshot
A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus
inferred← citeshttps://doi.org/10.3389/fpls.2020.584981openalex-snapshot
The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data
inferred← citeshttps://doi.org/10.3390/biology11010091openalex-snapshot
Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis
inferred← citeshttps://doi.org/10.3390/toxins15110650openalex-snapshot
Venomous Noodles: The Evolution of Toxins in Nemertea through Positive Selection and Gene Duplication
inferred← citeshttps://doi.org/10.3390/v13091694openalex-snapshot
Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies
inferred← citeshttps://doi.org/10.3410/f.734380463.793553343openalex-snapshot
Faculty Opinions recommendation of Tempo and mode of genome evolution in the budding yeast subphylum.
inferred← citeshttps://doi.org/10.3410/f.734380463.793554773openalex-snapshot
Faculty Opinions recommendation of Tempo and mode of genome evolution in the budding yeast subphylum.
inferred← citeshttps://doi.org/10.4137/ebo.s14239openalex-snapshot
TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information
inferred← citeshttps://doi.org/10.48550/arxiv.1903.04530openalex-snapshot
Orthology: definitions, inference, and impact on species phylogeny inference
inferred← citeshttps://doi.org/10.70675/2f48e6ddza822z455eza9d5zf10fc679949copenalex-snapshot
Le défi évolutif du changement climatique, processus adaptatifs chez le corail rouge (Corallium rubrum)
inferred← citeshttps://doi.org/10.7287/peerj.11019v0.1/reviews/1openalex-snapshot
Peer Review #1 of "New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.11019v0.1/reviews/2openalex-snapshot
Peer Review #2 of "New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.11019v0.1/reviews/3openalex-snapshot
Peer Review #3 of "New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.11019v0.2/reviews/1openalex-snapshot
Peer Review #1 of "New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.11019v0.2/reviews/2openalex-snapshot
Peer Review #2 of "New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.1719v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Spider phylogenomics: untangling the Spider Tree of Life (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4842v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4842v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4842v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4842v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.4842v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.4842v0.2/reviews/3openalex-snapshot
Peer Review #3 of "Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.11019openalex-snapshot
New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics
inferred← citeshttps://doi.org/10.7717/peerj.1719openalex-snapshot
Spider phylogenomics: untangling the Spider Tree of Life
inferred← citeshttps://doi.org/10.7717/peerj.4842openalex-snapshot
Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs
inferred← citeshttps://doi.org/10.9734/ijpss/2023/v35i203792openalex-snapshot
Deciphering Millet Diversity: Proteomic Clusters and Phylogenetic Insights
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
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