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An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

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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/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/bf02603120openalex-snapshot

Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

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.patrec.2005.10.010openalex-snapshot

An introduction to ROC analysis

inferredcites →https://doi.org/10.1073/pnas.2335847100openalex-snapshot

Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster

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

Joint Bayesian Estimation of Alignment and Phylogeny

inferredcites →https://doi.org/10.1080/10635150701472164openalex-snapshot

Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments

inferredcites →https://doi.org/10.1093/bioinformatics/14.2.157openalex-snapshot

Rose: generating sequence families.

inferredcites →https://doi.org/10.1093/bioinformatics/17.6.573openalex-snapshot

SOAP, cleaning multiple alignments from unstable blocks

inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s71openalex-snapshot

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues

inferredcites →https://doi.org/10.1093/bioinformatics/8.3.275openalex-snapshot

The rapid generation of mutation data matrices from protein sequences

inferredcites →https://doi.org/10.1093/bioinformatics/bti623openalex-snapshot

ROCR: visualizing classifier performance in R

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/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/27.13.2682openalex-snapshot

A comprehensive comparison of multiple sequence alignment programs

inferredcites →https://doi.org/10.1093/nar/gkg522openalex-snapshot

Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments

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/gki198openalex-snapshot

MAFFT version 5: improvement in accuracy of multiple sequence alignment

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/oxfordjournals.molbev.a040454openalex-snapshot

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

inferredcites →https://doi.org/10.1111/j.1558-5646.1985.tb00420.xopenalex-snapshot

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

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/10.1137/0148063openalex-snapshot

The Multiple Sequence Alignment Problem in Biology

inferredcites →https://doi.org/10.1142/9789812776136_0003openalex-snapshot

LOCAL RELIABILITY MEASURES FROM SETS OF CO-OPTIMAL MULTIPLE SEQUENCE ALIGNMENTS

inferredcites →https://doi.org/10.1142/9789812776136_0004openalex-snapshot

THE EFFECT OF THE GUIDE TREE ON MULTIPLE SEQUENCE ALIGNMENTS AND SUBSEQUENT PHYLOGENETIC ANALYSES

inferredcites →https://doi.org/10.1186/1471-2105-6-83openalex-snapshot

Bayesian coestimation of phylogeny and sequence alignment

inferredcites →https://doi.org/10.1186/1471-2105-7-471openalex-snapshot

The accuracy of several multiple sequence alignment programs for proteins

inferredcites →https://doi.org/10.1371/journal.pcbi.1000392openalex-snapshot

Fast Statistical Alignment

What points at this work

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

inferred← citeshttps://doi.org/10.1002/tax.12718zenodo-depositor-declared

A phylogenetic survey of the ascomycete genus Arthrorhaphis (Arthrorhaphidaceae, Lecanoromycetes) including new species in Arthrorhaphis citrinella sensu lato

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlae028zenodo-depositor-declared

Multigene phylogeny and expanded morphological comparison reveal one new lineage and finer differentiation in the order Peniculida (Alveolata: Ciliophora)

inferred← citeshttps://doi.org/10.11646/phytotaxa.197.4.3zenodo-depositor-declared

A new species of Uleiorchis (Orchidaceae, Gastrodieae) from the Atlantic Forest of Brazil

inferred← citeshttps://doi.org/10.11646/phytotaxa.356.1.2zenodo-depositor-declared

Arthoniaceae with reddish, K+ purple ascomata in Japan

inferred← citeshttps://doi.org/10.11646/zootaxa.4000.4.4zenodo-depositor-declared

Phylogenetic positions of four hypotrichous ciliates (Protista, Ciliophora) based on SSU rRNA gene, with notes on their morphological characters

inferred← citeshttps://doi.org/10.2139/ssrn.4170516openalex-extracted

inferred← citeshttps://doi.org/10.1002/9781119072799.ch16openalex-snapshot

COMPARATIVE GENOMICS IN THE ASTERACEAE REVEALS LITTLE EVIDENCE FOR PARALLEL EVOLUTIONARY CHANGE IN INVASIVE TAXA

inferred← citeshttps://doi.org/10.1002/pro.2920openalex-snapshot

Intermediate divergence levels maximize the strength of structure–sequence correlations in enzymes and viral proteins

inferred← citeshttps://doi.org/10.1002/tax.616001openalex-snapshot

Molecular phylogeny and systematics of the Ocellularia clade (Ascomycota: Ostropales: Graphidaceae)

inferred← citeshttps://doi.org/10.1007/978-1-0716-3838-5_11openalex-snapshot

A Guide to Phylogenomic Inference

inferred← citeshttps://doi.org/10.1007/978-1-0716-3838-5_16openalex-snapshot

Comparative Evolutionary Genomics in Insects

inferred← citeshttps://doi.org/10.1007/978-1-4471-5298-9_6openalex-snapshot

Large-Scale Multiple Sequence Alignment and Phylogeny Estimation

inferred← citeshttps://doi.org/10.1007/978-1-4939-1438-8_4openalex-snapshot

A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome

inferred← citeshttps://doi.org/10.1007/978-1-4939-6622-6_14openalex-snapshot

Inferring Trees

inferred← citeshttps://doi.org/10.1007/978-1-4939-7151-0_21openalex-snapshot

Molecular Modeling of Transporters: From Low Resolution Cryo-Electron Microscopy Map to Conformational Exploration. The Example of TSPO

inferred← citeshttps://doi.org/10.1007/978-1-4939-7463-4_5openalex-snapshot

Phylogenomics

inferred← citeshttps://doi.org/10.1007/978-1-4939-9074-0_12openalex-snapshot

Selection Acting on Genomes

inferred← citeshttps://doi.org/10.1007/978-1-4939-9074-0_4openalex-snapshot

Whole-Genome Alignment

inferred← citeshttps://doi.org/10.1007/978-1-61779-582-4_7openalex-snapshot

Alignment Methods: Strategies, Challenges, Benchmarking, and Comparative Overview

inferred← citeshttps://doi.org/10.1007/978-1-61779-582-4_8openalex-snapshot

Whole-Genome Alignment

inferred← citeshttps://doi.org/10.1007/978-3-030-00834-5_17openalex-snapshot

Non-parametric and Semi-parametric Support Estimation Using SEquential RESampling Random Walks on Biomolecular Sequences

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

Alignment and Mapping

inferred← citeshttps://doi.org/10.1007/978-3-319-64198-0_6openalex-snapshot

Comparative Genomics of Soybean and Other Legumes

inferred← citeshttps://doi.org/10.1007/978-3-319-64918-4_1openalex-snapshot

Introduction and Background

inferred← citeshttps://doi.org/10.1007/978-3-319-64918-4_6openalex-snapshot

Parameter Advising for the Opal Aligner

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/10.1007/978-3-642-29627-7_5openalex-snapshot

Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising

inferred← citeshttps://doi.org/10.1007/978-3-662-58811-6_2openalex-snapshot

Wie funktionieren MSA-Programme?

inferred← citeshttps://doi.org/10.1007/978-3-662-64473-7_2openalex-snapshot

How Do MSA Programs Work?

inferred← citeshttps://doi.org/10.1007/978-981-16-3993-7_9openalex-snapshot

Phylogenetic Analysis

inferred← citeshttps://doi.org/10.1007/s00239-012-9538-8openalex-snapshot

Membrane Environment Imposes Unique Selection Pressures on Transmembrane Domains of G Protein-Coupled Receptors

inferred← citeshttps://doi.org/10.1007/s00239-013-9589-5openalex-snapshot

Molecular Evolutionary Analysis of Vertebrate Transducins: A Role for Amino Acid Variation in Photoreceptor Deactivation

inferred← citeshttps://doi.org/10.1007/s00343-015-4083-0openalex-snapshot

Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the well-known genus Zoothamnium (Ciliophora, Peritrichia)

inferred← citeshttps://doi.org/10.1007/s00343-019-7277-zopenalex-snapshot

Molecular phylogeny and Ultrastructure of a new population of Urostyla grandis (Ciliophora, Hypotrichida) from Harbin, China

inferred← citeshttps://doi.org/10.1007/s10750-017-3371-4openalex-snapshot

Reconsideration of the systematics of Peniculida (Protista, Ciliophora) based on SSU rRNA gene sequences and new morphological features of Marituja and Disematostoma

inferred← citeshttps://doi.org/10.1007/s10750-022-05044-yopenalex-snapshot

Genetic population structure of the blue sea star (Linckia laevigata) and the boring giant clam (Tridacna crocea) across Malaysia

inferred← citeshttps://doi.org/10.1007/s11262-015-1273-yopenalex-snapshot

Expression of a second open reading frame present in the genome of tick-borne encephalitis virus strain Neudoerfl is not detectable in infected cells

inferred← citeshttps://doi.org/10.1007/s11427-020-1817-5openalex-snapshot

New contributions to the phylogeny of the ciliate class Heterotrichea (Protista, Ciliophora): analyses at family-genus level and new evolutionary hypotheses

inferred← citeshttps://doi.org/10.1007/s11557-017-1374-1openalex-snapshot

Production of the bioactive pigment elsinochrome A by a cultured mycobiont strain of the lichen Graphis elongata

inferred← citeshttps://doi.org/10.1007/s11756-023-01574-5openalex-snapshot

Elucidation of population structure of Culicoides oxystoma a vector of BTV in India and its genetic variability within conspecifics

inferred← citeshttps://doi.org/10.1007/s13225-013-0230-0openalex-snapshot

Molecular phylogeny of the genus Sticta (lichenized Ascomycota: Lobariaceae) in Colombia

inferred← citeshttps://doi.org/10.1007/s13225-013-0267-0openalex-snapshot

Lepidostromatales, a new order of lichenized fungi (Basidiomycota, Agaricomycetes), with two new genera, Ertzia and Sulzbacheromyces, and one new species, Lepidostroma winklerianum

inferred← citeshttps://doi.org/10.1007/s13225-017-0380-6openalex-snapshot

High levels of endemism among Galapagos basidiolichens

inferred← citeshttps://doi.org/10.1007/s13225-017-0382-4openalex-snapshot

Dismantling Marchandiomphalina into Agonimia (Verrucariaceae) and Lawreymyces gen. nov. (Corticiaceae): setting a precedent to the formal recognition of thousands of voucherless fungi based on type sequences

inferred← citeshttps://doi.org/10.1007/s42995-022-00142-1openalex-snapshot

Phylogeny of the anaerobic ciliate genus Sonderia (Protista: Ciliophora: Plagiopylea), including the description of three novel species and a brief revision of the genus

inferred← citeshttps://doi.org/10.1007/s42995-022-00152-zopenalex-snapshot

The widely reported but poorly studied ciliate family Folliculinidae (Protozoa, Ciliophora, Heterotrichea): a revision with notes on its taxonomy, morphology and phylogenetic relationships

inferred← citeshttps://doi.org/10.1007/s42995-023-00175-0openalex-snapshot

Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms

inferred← citeshttps://doi.org/10.1007/s42995-024-00266-6openalex-snapshot

Investigating the psammophilic karyorelictean ciliate families Kentrophoridae and Cryptopharyngidae (Protista, Ciliophora): molecular phylogeny, geographic distributions and a brief revision including descriptions of a new genus, a new species and a new combination

inferred← citeshttps://doi.org/10.1007/s42995-026-00376-3openalex-snapshot

Notes on the life cycle of a new marine ciliate, Metafolliculina songi n. sp. (Protozoa, Ciliophora, Heterotrichea), with description of its infraciliature and phylogeny

inferred← citeshttps://doi.org/10.1016/b978-0-12-813012-4.00023-1openalex-snapshot

Ediacarans, Protolichens, and Lichen-Derived Penicillium

inferred← citeshttps://doi.org/10.1016/j.biotechadv.2016.03.001openalex-snapshot

Making sense of genomes of parasitic worms: Tackling bioinformatic challenges

inferred← citeshttps://doi.org/10.1016/j.cell.2015.11.008openalex-snapshot

The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan

inferred← citeshttps://doi.org/10.1016/j.dnarep.2014.07.005openalex-snapshot

Sequence divergence and diversity suggests ongoing functional diversification of vertebrate NAD metabolism

inferred← citeshttps://doi.org/10.1016/j.ejop.2012.01.007openalex-snapshot

Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea)

inferred← citeshttps://doi.org/10.1016/j.ejop.2015.06.008openalex-snapshot

Estimation of divergence times in litostomatean ciliates (Ciliophora: Intramacronucleata), using Bayesian relaxed clock and 18S rRNA gene

inferred← citeshttps://doi.org/10.1016/j.ejop.2015.08.003openalex-snapshot

Morphology of three Litonotus species (Ciliophora: Pleurostomatida) from China seas, with brief notes on their SSU rDNA-based phylogeny

inferred← citeshttps://doi.org/10.1016/j.ejop.2016.04.004openalex-snapshot

Description of two marine amphisiellid ciliates, Amphisiella milnei (Kahl, 1932) Horváth, 1950 and A. sinica sp. nov. (Ciliophora: Hypotrichia), with notes on their ontogenesis and SSU rDNA-based phylogeny

inferred← citeshttps://doi.org/10.1016/j.ejop.2016.08.005openalex-snapshot

Morphology of four cyrtophorian ciliates (Protozoa, Ciliophora) from Yangtze Delta, China, with notes on the phylogeny of the genus Phascolodon

inferred← citeshttps://doi.org/10.1016/j.ejop.2017.11.001openalex-snapshot

Morphology, cell-division, and phylogeny of Schmidingerothrix elongata spec. nov. (Ciliophora, Hypotricha), and brief guide to hypotrichs with Gonostomum -like oral apparatus

inferred← citeshttps://doi.org/10.1016/j.ejop.2018.09.002openalex-snapshot

The affiliation of Hexasterias problematica and Halodinium verrucatum sp. nov. to ciliate cysts based on molecular phylogeny and cyst wall composition

inferred← citeshttps://doi.org/10.1016/j.ejop.2019.05.001openalex-snapshot

Taxonomy and phylogeny of two poorly studied genera of marine oligotrich ciliates including descriptions of two new species: Cyrtostrombidium paraboreale sp. n. and Apostrombidium orientale sp. n. (Ciliophora: Spirotrichea)

inferred← citeshttps://doi.org/10.1016/j.ejop.2021.125769openalex-snapshot

Taxonomy, phylogeny, and geographical distribution of the little-known Helicoprorodon multinucleatum Dragesco, 1960 (Ciliophora, Haptorida) and key to species within the genus

inferred← citeshttps://doi.org/10.1016/j.ejop.2022.125864openalex-snapshot

Morphogenesis and molecular phylogeny of a freshwater ciliate, Oxytricha multilineata n. sp. (Ciliophora, Hypotrichia)

inferred← citeshttps://doi.org/10.1016/j.ejop.2023.126003openalex-snapshot

First redescription and molecular phylogeny of Trimyema claviforme Kahl, 1933 with the description of a Chinese population of Plagiopyla nasuta Stein, 1860 (Ciliophora, Plagiopylea)

inferred← citeshttps://doi.org/10.1016/j.febslet.2014.10.008openalex-snapshot

The vertebrate muscle‐specific RING finger protein family includes MuRF4 – A novel, conserved E3‐ubiquitin ligase

inferred← citeshttps://doi.org/10.1016/j.fsi.2016.12.024openalex-snapshot

Characterisation of arginase paralogues in salmonids and their modulation by immune stimulation/ infection

inferred← citeshttps://doi.org/10.1016/j.fsi.2019.07.019openalex-snapshot

Expansion and loss events characterized the occurrence of MIF-like genes in bivalves

inferred← citeshttps://doi.org/10.1016/j.funbio.2013.05.006openalex-snapshot

Starting from scratch: Evolution of the lichen thallus in the basidiolichen Dictyonema (Agaricales: Hygrophoraceae)

inferred← citeshttps://doi.org/10.1016/j.gene.2014.07.061openalex-snapshot

Molecular evolution of growth hormone and insulin-like growth factor 1 receptors in long-lived, small-bodied mammals

inferred← citeshttps://doi.org/10.1016/j.gene.2019.03.008openalex-snapshot

Genome-wide analyses reveal genes subject to positive selection in Toxoplasma gondii

inferred← citeshttps://doi.org/10.1016/j.isci.2023.107832openalex-snapshot

Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond

inferred← citeshttps://doi.org/10.1016/j.jgg.2021.05.014openalex-snapshot

Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer

inferred← citeshttps://doi.org/10.1016/j.meegid.2016.03.008openalex-snapshot

Molecular identification of Borrelia genus in questing hard ticks from Portugal: Phylogenetic characterization of two novel Relapsing Fever-like Borrelia sp.

inferred← citeshttps://doi.org/10.1016/j.molimm.2018.04.011openalex-snapshot

Genomic organization and adaptive evolution of IGHC genes in marine mammals

inferred← citeshttps://doi.org/10.1016/j.parint.2017.01.006openalex-snapshot

Parasciadicleithrum octofasciatum n. gen., n. sp. (Monogenoidea: Dactylogyridae), parasite of Rocio octofasciata (Regan) (Cichlidae: Perciformes) from Mexico characterised by morphological and molecular evidence

inferred← citeshttps://doi.org/10.1016/j.parint.2017.09.012openalex-snapshot

A new genus and two new species of dactylogyrid monogeneans from gills of Neotropical catfishes (Siluriformes: Doradidae and Loricariidae)

inferred← citeshttps://doi.org/10.1016/j.protis.2022.125867openalex-snapshot

Ultrastructure of Apocolpodidium etoschense (Ciliophora) and its Systematics Enlightenment for the Class Nassophorea

inferred← citeshttps://doi.org/10.1016/j.sbi.2023.102577openalex-snapshot

Towards the accurate alignment of over a million protein sequences: Current state of the art

inferred← citeshttps://doi.org/10.1016/j.tig.2020.07.008openalex-snapshot

Studying Natural Selection in the Era of Ubiquitous Genomes

inferred← citeshttps://doi.org/10.1016/j.ttbdis.2016.09.015openalex-snapshot

Multiple Phlebovirus (Bunyaviridae) genetic groups detected in Rhipicephalus, Hyalomma and Dermacentor ticks from southern Portugal

inferred← citeshttps://doi.org/10.1016/j.virol.2015.04.021openalex-snapshot

Negeviruses found in multiple species of mosquitoes from southern Portugal: Isolation, genetic diversity, and replication in insect cell culture

inferred← citeshttps://doi.org/10.1016/j.ygcen.2014.03.002openalex-snapshot

Evolution of receptors for peptides similar to glucagon

inferred← citeshttps://doi.org/10.1016/j.ympev.2011.04.025openalex-snapshot

Parallel evolution and phenotypic divergence in lichenized fungi: A case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales)

inferred← citeshttps://doi.org/10.1016/j.ympev.2012.06.008openalex-snapshot

Phylogeny, integration and expression of sigma virus-like genes in Drosophila

inferred← citeshttps://doi.org/10.1016/j.ympev.2013.03.018openalex-snapshot

Multigene-based analyses on evolutionary phylogeny of two controversial ciliate orders: Pleuronematida and Loxocephalida (Protista, Ciliophora, Oligohymenophorea)

inferred← citeshttps://doi.org/10.1016/j.ympev.2013.10.001openalex-snapshot

Phylogenomic analyses support the bifurcation of ciliates into two major clades that differ in properties of nuclear division

inferred← citeshttps://doi.org/10.1016/j.ympev.2014.01.032openalex-snapshot

Phylogenetic analyses of cyclidiids (Protista, Ciliophora, Scuticociliatia) based on multiple genes suggest their close relationship with thigmotrichids

inferred← citeshttps://doi.org/10.1016/j.ympev.2014.02.022openalex-snapshot

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.2015.04.027openalex-snapshot

Fleas (Siphonaptera) are Cretaceous, and evolved with Theria

inferred← citeshttps://doi.org/10.1016/j.ympev.2016.02.009openalex-snapshot

A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece

inferred← citeshttps://doi.org/10.1016/j.ympev.2016.05.007openalex-snapshot

Multigene-based phylogeny of the ciliate families Amphisiellidae and Trachelostylidae (Protozoa: Ciliophora: Hypotrichia)

inferred← citeshttps://doi.org/10.1016/j.ympev.2017.04.018openalex-snapshot

Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.02.002openalex-snapshot

Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107380openalex-snapshot

Phylogenetic revision of the lichenized family Gomphillaceae (Ascomycota: Graphidales) suggests post-K–Pg boundary diversification and phylogenetic signal in asexual reproductive structures

inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107433openalex-snapshot

Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea)

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108468openalex-snapshot

An integrated framework for evolution of ciliated protists (Protista, Ciliophora) from the perspective of comparative genomics

inferred← citeshttps://doi.org/10.1017/s0022149x2100016xopenalex-snapshot

New perspectives on Aspersentis Megarhynchus (Acanthocephala: Heteracanthocephalidae) from Notothenia Coriiceps Richardson (Nototheniidae) in the West Antarctic, with emended generic diagnosis

inferred← citeshttps://doi.org/10.1017/s0024282912000825openalex-snapshot

Phylogeny of the Lobariaceae (lichenized Ascomycota: Peltigerales), with a reappraisal of the genus Lobariella

inferred← citeshttps://doi.org/10.1017/s0024282913000583openalex-snapshot

New lichen-associated bulbil-forming species of Cantharellales (Basidiomycetes)

inferred← citeshttps://doi.org/10.1017/s0024282915000146openalex-snapshot

The status of the conservation priority species Calicium corynellum in the British Isles

inferred← citeshttps://doi.org/10.1017/s0024282916000505openalex-snapshot

A phylogenetic framework for reassessing generic concepts and species delimitation in the lichenized familyTrypetheliaceae(Ascomycota: Dothideomycetes)

inferred← citeshttps://doi.org/10.1017/s0024282916000645openalex-snapshot

Geographically disjunct phylogenetic lineages inLeptogium hibernicumrevealLeptogium krogiaesp. nov. from East Africa

inferred← citeshttps://doi.org/10.1017/s0024282917000378openalex-snapshot

A hidden basidiolichen rediscovered:Omphalina oreadesis a separate species in the genusLichenomphalia(Basidiomycota:Agaricales:Hygrophoraceae)

inferred← citeshttps://doi.org/10.1017/s0024282917000470openalex-snapshot

The genusLobariella(Ascomycota:Lobariaceae) in Hawaii: late colonization, high inferred endemism and three new species resulting from “micro-radiation”

inferred← citeshttps://doi.org/10.1017/s002428291900046xopenalex-snapshot

Symbiont composition of the basidiolichen Lichenomphalia meridionalis varies with altitude in the Iberian Peninsula

inferred← citeshttps://doi.org/10.1017/s0031182022001007openalex-snapshot

Hexabothriidae and Monocotylidae (Monogenoidea) from the gills of neonate hammerhead sharks (Sphyrnidae) Sphyrna gilberti, Sphyrna lewini and their hybrids from the western North Atlantic Ocean

inferred← citeshttps://doi.org/10.1038/emi.2016.94openalex-snapshot

Detection of spring viraemia of carp virus in imported amphibians reveals an unanticipated foreign animal disease threat

inferred← citeshttps://doi.org/10.1038/hdy.2014.32openalex-snapshot

Insights into the history of a bacterial group II intron remnant from the genomes of the nitrogen-fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae

inferred← citeshttps://doi.org/10.1038/s41467-020-16366-7openalex-snapshot

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

inferred← citeshttps://doi.org/10.1038/s41598-018-36048-1openalex-snapshot

Molecular evolution of juvenile hormone esterase-like proteins in a socially exchanged fluid

inferred← citeshttps://doi.org/10.1038/srep34806openalex-snapshot

The complete salmonid IGF-IR gene repertoire and its transcriptional response to disease

inferred← citeshttps://doi.org/10.1080/0028825x.2017.1364274openalex-snapshot

Lecanora kohu , a new species of Lecanora (lichenised Ascomycota: Lecanoraceae) from the Chatham Islands, New Zealand

inferred← citeshttps://doi.org/10.1080/14772000.2015.1081992openalex-snapshot

Biodiversity of oligotrich ciliates in the South China Sea: description of three newStrombidiumspecies (Protozoa, Ciliophora, Oligotrichia) with phylogenetic analyses

inferred← citeshttps://doi.org/10.1080/15435075.2016.1277728openalex-snapshot

Potential biodiesel-producing microalgae: two new strains of Amphikrikos sp.

inferred← citeshttps://doi.org/10.1089/cmb.2013.0007openalex-snapshot

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

inferred← citeshttps://doi.org/10.1089/cmb.2022.0197openalex-snapshot

Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting

inferred← citeshttps://doi.org/10.1093/bib/bbv099openalex-snapshot

Multiple sequence alignment modeling: methods and applications

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab263openalex-snapshot

Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited

inferred← citeshttps://doi.org/10.1093/bioinformatics/btae196openalex-snapshot

Effect of tokenization on transformers for biological sequences

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

Measuring the distance between multiple sequence alignments

inferred← citeshttps://doi.org/10.1093/bioinformatics/btw108openalex-snapshot

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

inferred← citeshttps://doi.org/10.1093/bioinformatics/btw412openalex-snapshot

Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

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/botlinnean/box016openalex-snapshot

Genome size dynamics in tribe Gilliesieae (Amaryllidaceae, subfamily Allioideae) in the context of polyploidy and unusual incidence of Robertsonian translocations

inferred← citeshttps://doi.org/10.1093/femsle/fnv127openalex-snapshot

Diversity ofRhodopirellulaand related planctomycetes in a North Sea coastal sediment employingcarBas molecular marker

inferred← citeshttps://doi.org/10.1093/gbe/evaa164openalex-snapshot

Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy

inferred← citeshttps://doi.org/10.1093/gbe/evae093openalex-snapshot

Insertion–Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure

inferred← citeshttps://doi.org/10.1093/gbe/evr100openalex-snapshot

Red and Problematic Green Phylogenetic Signals among Thousands of Nuclear Genes from the Photosynthetic and Apicomplexa-Related Chromera velia

inferred← citeshttps://doi.org/10.1093/gbe/evs053openalex-snapshot

Reevaluating the Green Contribution to Diatom Genomes

inferred← citeshttps://doi.org/10.1093/gbe/evt195openalex-snapshot

Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past

inferred← citeshttps://doi.org/10.1093/gbe/evu157openalex-snapshot

Highly Variable Recombinational Landscape Modulates Efficacy of Natural Selection in Birds

inferred← citeshttps://doi.org/10.1093/gbe/evu252openalex-snapshot

Indel Reliability in Indel-Based Phylogenetic Inference

inferred← citeshttps://doi.org/10.1093/gbe/evv149openalex-snapshot

Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality

inferred← citeshttps://doi.org/10.1093/gbe/evw200openalex-snapshot

Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns

inferred← citeshttps://doi.org/10.1093/gbe/evx002openalex-snapshot

Amoebozoans are Secretly but Ancestrally Sexual: Evidence for Sex Genes and Potential Novel Crossover Pathways in Diverse Groups of Amoebae

inferred← citeshttps://doi.org/10.1093/gbe/evy131openalex-snapshot

Neofunctionalization in Ligand Binding Sites of Ant Olfactory Receptors

inferred← citeshttps://doi.org/10.1093/gbe/evy204openalex-snapshot

Evolution of olfactory functions on the fire ant social chromosome

inferred← citeshttps://doi.org/10.1093/jme/tjaf039openalex-snapshot

Genetic analyses of Culicoides peregrinus (Diptera: Ceratopogonidae) reveal population differentiation in southern India a hotspot of bluetongue disease outbreaks and lack of gene flow across its range

inferred← citeshttps://doi.org/10.1093/molbev/msaa312openalex-snapshot

The Molecular Determinants of Thermoadaptation:Methanococcalesas a Case Study

inferred← citeshttps://doi.org/10.1093/molbev/msab146openalex-snapshot

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties

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/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/mst272openalex-snapshot

Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes

inferred← citeshttps://doi.org/10.1093/molbev/msu055openalex-snapshot

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

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/msu141openalex-snapshot

Patterns of Positive Selection in Seven Ant Genomes

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/msu183openalex-snapshot

Limited Utility of Residue Masking for Positive-Selection Inference

inferred← citeshttps://doi.org/10.1093/molbev/msu231openalex-snapshot

Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies

inferred← citeshttps://doi.org/10.1093/molbev/msv175openalex-snapshot

Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis

inferred← citeshttps://doi.org/10.1093/molbev/msy055openalex-snapshot

Alignment Modulates Ancestral Sequence Reconstruction Accuracy

inferred← citeshttps://doi.org/10.1093/molbev/msy161openalex-snapshot

Limited Evidence for Parallel Molecular Adaptations Associated with the Subterranean Niche in Mammals: A Comparative Study of Three Superorders

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/gkq443openalex-snapshot

GUIDANCE: a web server for assessing alignment confidence scores

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/gkt1065openalex-snapshot

Selectome update: quality control and computational improvements to a database of positive selection

inferred← citeshttps://doi.org/10.1093/nar/gkv310openalex-snapshot

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction: Figure 1.

inferred← citeshttps://doi.org/10.1093/nar/gkv318openalex-snapshot

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

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/nargab/lqaa041openalex-snapshot

A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

inferred← citeshttps://doi.org/10.1093/sysbio/syt016openalex-snapshot

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

inferred← citeshttps://doi.org/10.1093/sysbio/syw074openalex-snapshot

Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking

inferred← citeshttps://doi.org/10.1093/sysbio/syw101openalex-snapshot

Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses

inferred← citeshttps://doi.org/10.1093/sysbio/syx096openalex-snapshot

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

inferred← citeshttps://doi.org/10.1093/sysbio/syy036openalex-snapshot

Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlaa145openalex-snapshot

Some morphologically distinguishable hypotrich ciliates share identical 18S rRNA gene sequences – taxonomic insights from a case study onOxytrichaspecies (Protista, Ciliophora)

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlad015openalex-snapshot

Molecular phylogeny and taxonomy of three anaerobic plagiopyleans (Alveolata: Ciliophora), retrieved from two geographically distant localities in Asia and North America

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlae055openalex-snapshot

Ontogeny and phylogeny of the anaerobic genus Urostomides with supplementing morphological characterization of the type and one little-known species (Alveolata: Ciliophora: Armophorea)

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlw006openalex-snapshot

Phylogeny and taxonomy of five poorly known species of cyrtophorian ciliates (Protozoa: Ciliophora: Phyllopharyngea) from China Seas

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlz115openalex-snapshot

A new contribution to the taxonomy and molecular phylogeny of three, well-known freshwater species of the ciliate genus Spirostomum (Protozoa: Ciliophora: Heterotrichea)

inferred← citeshttps://doi.org/10.1098/rsob.130219openalex-snapshot

Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses

inferred← citeshttps://doi.org/10.1098/rspb.2012.2968openalex-snapshot

Duplication and concerted evolution in a master sex determiner under balancing selection

inferred← citeshttps://doi.org/10.1098/rstb.2013.0088openalex-snapshot

Early bioenergetic evolution

inferred← citeshttps://doi.org/10.1099/ijs.0.000377openalex-snapshot

Reconsideration of the ‘well-known’ hypotrichous ciliate Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003 (Ciliophora, Sporadotrichida), with notes on its morphology, morphogenesis and molecular phylogeny

inferred← citeshttps://doi.org/10.1099/ijs.0.059899-0openalex-snapshot

Morphological reports on two species of Dexiotricha (Ciliophora, Scuticociliatia), with a note on the phylogenetic position of the genus

inferred← citeshttps://doi.org/10.1099/ijs.0.062026-0openalex-snapshot

Morphological and molecular characterization of Parafurgasonia zhangi spec. nov. and Chilodonella acuta Kahl, 1931 (Protozoa, Ciliophora), from a soil habitat of Saudi Arabia

inferred← citeshttps://doi.org/10.1099/ijs.0.068783-0openalex-snapshot

Morphology and phylogeny of three karyorelictean ciliates (Protista, Ciliophora), including two novel species, Trachelocerca chinensis sp. n. and Tracheloraphis dragescoi sp. n.

inferred← citeshttps://doi.org/10.1099/ijsem.0.000651openalex-snapshot

Morphology and molecular phylogeny of Pleuronema orientale spec. nov. and Pleuronema paucisaetosum spec. nov. (Ciliophora, Scuticociliata) from Hangzhou Bay, China

inferred← citeshttps://doi.org/10.1101/074831openalex-snapshot

HDP-Align: Hierarchical Dirichlet Process Clustering for Multiple Peak Alignment of Liquid Chromatography Mass Spectrometry Data

inferred← citeshttps://doi.org/10.1101/2021.08.04.455051openalex-snapshot

Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty

inferred← citeshttps://doi.org/10.1101/2022.07.22.501063openalex-snapshot

Harnessing machine translation methods for sequence alignment

inferred← citeshttps://doi.org/10.1101/gr.174920.114openalex-snapshot

Alignathon: a competitive assessment of whole-genome alignment methods

inferred← citeshttps://doi.org/10.1101/gr.272310.120openalex-snapshot

The genomic basis of evolutionary differentiation among honey bees

inferred← citeshttps://doi.org/10.1104/pp.114.239137openalex-snapshot

Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family

inferred← citeshttps://doi.org/10.1104/pp.15.01470openalex-snapshot

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

inferred← citeshttps://doi.org/10.1109/tcbb.2015.2430323openalex-snapshot

Learning Parameter-Advising Sets for Multiple Sequence Alignment

inferred← citeshttps://doi.org/10.1111/boj.12415openalex-snapshot

Narrow water barriers prevent multiple colonizations and limit gene flow among California Channel Island wild buckwheats (Eriogonum: Polygonaceae)

inferred← citeshttps://doi.org/10.1111/brv.12390openalex-snapshot

Bayesian molecular dating: opening up the black box

inferred← citeshttps://doi.org/10.1111/cla.12167openalex-snapshot

Phylogenetic reconstruction based on COI reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes

inferred← citeshttps://doi.org/10.1111/evo.12935openalex-snapshot

Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa

inferred← citeshttps://doi.org/10.1111/j.1365-3113.2012.00624.xopenalex-snapshot

Origin and diversification of the cryptic ant genus Stenamma Westwood (Hymenoptera: Formicidae), inferred from multilocus molecular data, biogeography and natural history

inferred← citeshttps://doi.org/10.1111/j.1463-6409.2012.00568.xopenalex-snapshot

Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships within the Mobilida (Ciliophora, Oligohymenophorea)

inferred← citeshttps://doi.org/10.1111/j.1550-7408.2011.00590.xopenalex-snapshot

Complete r RNA Sequence, Arrangement of Tandem Repeated Units and Phylogeny of N osema fumiferanae from Spruce Budworm, C horistoneura fumiferana ( C lemens)

inferred← citeshttps://doi.org/10.1111/jeu.12005openalex-snapshot

Three New L oxophyllum Species ( C iliophora: P leurostomatida) from C hina with a Brief Review of the Marine and Brackish L oxophyllum Species

inferred← citeshttps://doi.org/10.1111/jeu.12146openalex-snapshot

Morphology of Three Species of Amphileptus (Protozoa, Ciliophora, Pleurostomatida) from the South China Sea, with Note on Phylogeny of A. dragescoi sp. n.

inferred← citeshttps://doi.org/10.1111/jeu.12199openalex-snapshot

Sapocribrum chincoteaguense n. gen. n. sp.: A Small, Scale‐bearing Amoebozoan with Flabellinid Affinities

inferred← citeshttps://doi.org/10.1111/jeu.12277openalex-snapshot

Morphology and Phylogeny of Three Pleuronema Species (Ciliophora, Scuticociliatia) from Hangzhou Bay, China, with Description of Two New Species, P. binucleatum n. sp. and P. parawiackowskii n. sp.

inferred← citeshttps://doi.org/10.1111/jeu.12344openalex-snapshot

Morphology and Molecular Phylogeny of Two Poorly Known Species of Protocruzia (Ciliophora: Protocruziida)

inferred← citeshttps://doi.org/10.1111/jeu.12431openalex-snapshot

Morphology and Phylogeny of Two Novel Ciliates, Arcanisutura chongmingensis n. gen., n. sp. and Naxella paralucida n. sp. from Shanghai, China

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