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  1. Article ; Online: On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference.

    Criscuolo, Alexis

    F1000Research

    2020  Volume 9, Page(s) 1309

    Abstract: Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations in practice to approximating uncorrected distances ... ...

    Abstract Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations in practice to approximating uncorrected distances between genomes, and transforming these pairwise dissimilarities into proper evolutionary distances. It is notably shown that complex distance measures can be easily approximated using simple transformation formulae based on few parameters. MinHash-based techniques can therefore be very useful for implementing fast yet accurate alignment-free phylogenetic reconstruction procedures from large sets of genomes. This last point of view is assessed with a simulation study using a dedicated bioinformatics tool.
    MeSH term(s) Biological Evolution ; Computational Biology ; Evolution, Molecular ; Genome ; Phylogeny
    Language English
    Publishing date 2020-11-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.26930.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

    Criscuolo, Alexis

    Research Ideas and Outcomes. 2019 June 10, v. 5

    2019  

    Abstract: This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools. For each pair of genomes, a dissimilarity measure is first computed and next ...

    Abstract This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution. These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch. Analyses of both simulated and real genome datasets show that this bioinformatics procedure allows accurate phylogenetic trees to be reconstructed with fast running times, especially when launched on multiple threads. Implemented in a publicly available script, named JolyTree, this procedure is a useful approach for quickly inferring species trees without the burden and potential biases of multiple sequence alignments.
    Keywords bioinformatics ; data collection ; genome ; phylogeny ; research
    Language English
    Dates of publication 2019-0610
    Publishing place Pensoft Publishers
    Document type Article
    ZDB-ID 2833254-4
    ISSN 2367-7163
    ISSN 2367-7163
    DOI 10.3897/rio.5.e36178
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: morePhyML: improving the phylogenetic tree space exploration with PhyML 3.

    Criscuolo, Alexis

    Molecular phylogenetics and evolution

    2011  Volume 61, Issue 3, Page(s) 944–948

    Abstract: PhyML is a widely used Maximum Likelihood (ML) phylogenetic tree inference software based on a standard hill-climbing method. Starting from an initial tree, the version 3 of PhyML explores the tree space by using "Nearest Neighbor Interchange" (NNI) or " ... ...

    Abstract PhyML is a widely used Maximum Likelihood (ML) phylogenetic tree inference software based on a standard hill-climbing method. Starting from an initial tree, the version 3 of PhyML explores the tree space by using "Nearest Neighbor Interchange" (NNI) or "Subtree Pruning and Regrafting" (SPR) tree swapping techniques in order to find the ML phylogenetic tree. NNI-based local searches are fast but can often get trapped in local optima, whereas it is expected that the larger (but slower to cover) SPR-based neighborhoods will lead to trees with higher likelihood. Here, I verify that PhyML infers more likely trees with SPRs than with NNIs in almost all cases. However, I also show that the SPR-based local search of PhyML often does not succeed at locating the ML tree. To improve the tree space exploration, I deliver a script, named morePhyML, which allows escaping from local optima by performing character reweighting. This ML tree search strategy, named ratchet, often leads to higher likelihood estimates. Based on the analysis of a large number of amino acid and nucleotide data, I show that morePhyML allows inferring more accurate phylogenetic trees than several other recently developed ML tree inference softwares in many cases.
    MeSH term(s) Computational Biology/methods ; Likelihood Functions ; Phylogeny ; Software ; Time Factors
    Language English
    Publishing date 2011-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 33610-5
    ISSN 1095-9513 ; 1055-7903
    ISSN (online) 1095-9513
    ISSN 1055-7903
    DOI 10.1016/j.ympev.2011.08.029
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Bacillus rhizoplanae

    Kämpfer, Peter / Lipski, André / McInroy, John A / Clermont, Dominique / Criscuolo, Alexis / Glaeser, Stefanie P

    International journal of systematic and evolutionary microbiology

    2022  Volume 72, Issue 7

    Abstract: A Gram-stain-positive, aerobic and endospore-forming bacterial strain, isolated from the root surface of maize ( ...

    Abstract A Gram-stain-positive, aerobic and endospore-forming bacterial strain, isolated from the root surface of maize (
    MeSH term(s) Bacillus ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Zea mays/microbiology
    Chemical Substances DNA, Bacterial ; Fatty Acids ; Peptidoglycan ; Phospholipids ; RNA, Ribosomal, 16S ; Diaminopimelic Acid (583-93-7)
    Language English
    Publishing date 2022-07-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2002336-4
    ISSN 1466-5034 ; 1466-5026
    ISSN (online) 1466-5034
    ISSN 1466-5026
    DOI 10.1099/ijsem.0.005450
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 409: Show issues Location:
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  5. Article ; Online: Sutcliffiella rhizosphaerae

    Kämpfer, Peter / Glaeser, Stefanie P / Lipski, André / McInroy, John A / Clermont, Dominique / Criscuolo, Alexis

    International journal of systematic and evolutionary microbiology

    2022  Volume 72, Issue 10

    Abstract: An aerobic, Gram-staining-positive, endospore-forming bacterium, isolated from the rhizosphere of roots of maize ( ...

    Abstract An aerobic, Gram-staining-positive, endospore-forming bacterium, isolated from the rhizosphere of roots of maize (
    MeSH term(s) Bacillaceae/genetics ; Bacterial Typing Techniques ; Base Composition ; Cardiolipins ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Nucleotides ; Peptidoglycan/chemistry ; Phosphatidylethanolamines ; Phospholipids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/chemistry ; Zea mays/microbiology
    Chemical Substances Cardiolipins ; DNA, Bacterial ; Fatty Acids ; Nucleotides ; Peptidoglycan ; Phosphatidylethanolamines ; Phospholipids ; RNA, Ribosomal, 16S ; Vitamin K 2 (11032-49-8) ; Diaminopimelic Acid (583-93-7)
    Language English
    Publishing date 2022-10-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2002336-4
    ISSN 1466-5034 ; 1466-5026
    ISSN (online) 1466-5034
    ISSN 1466-5026
    DOI 10.1099/ijsem.0.005590
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Neobacillus rhizosphaerae

    Kämpfer, Peter / Glaeser, Stefanie P / McInroy, John A / Clermont, Dominique / Lipski, André / Criscuolo, Alexis

    International journal of systematic and evolutionary microbiology

    2022  Volume 72, Issue 11

    Abstract: A Gram-stain-positive, facultative anaerobic endospore-forming bacterium, which originated from roots/rhizosphere of maize ( ...

    Abstract A Gram-stain-positive, facultative anaerobic endospore-forming bacterium, which originated from roots/rhizosphere of maize (
    MeSH term(s) Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Fatty Acids/chemistry ; Sequence Analysis, DNA ; Phospholipids/chemistry ; Bacillaceae ; Bacillus ; Zea mays/microbiology
    Chemical Substances RNA, Ribosomal, 16S ; DNA, Bacterial ; Fatty Acids ; Phospholipids
    Language English
    Publishing date 2022-11-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2002336-4
    ISSN 1466-5034 ; 1466-5026
    ISSN (online) 1466-5034
    ISSN 1466-5026
    DOI 10.1099/ijsem.0.005636
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 409: Show issues Location:
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  7. Article ; Online: Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays.

    Kämpfer, Peter / Lipski, André / Lamothe, Lucie / Clermont, Dominique / Criscuolo, Alexis / McInroy, John A / Glaeser, Stefanie P

    Antonie van Leeuwenhoek

    2023  Volume 116, Issue 9, Page(s) 883–892

    Abstract: A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ- ... ...

    Abstract A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246
    MeSH term(s) Zea mays/microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Base Composition ; Phylogeny ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; Vitamin K 2/metabolism ; Paenibacillus ; Fatty Acids/metabolism ; Bacterial Typing Techniques
    Chemical Substances RNA, Ribosomal, 16S ; DNA, Bacterial ; Vitamin K 2 (11032-49-8) ; Fatty Acids
    Language English
    Publishing date 2023-06-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 214861-4
    ISSN 1572-9699 ; 0003-6072
    ISSN (online) 1572-9699
    ISSN 0003-6072
    DOI 10.1007/s10482-023-01852-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Paenibacillus auburnensis

    Kämpfer, Peter / Lipski, André / McInroy, John A / Clermont, Dominique / Lamothe, Lucie / Glaeser, Stefanie P / Criscuolo, Alexis

    International journal of systematic and evolutionary microbiology

    2023  Volume 73, Issue 4

    Abstract: Two Gram-stain-positive, aerobic, endospore-forming bacterial strains, isolated from the rhizosphere ... ...

    Abstract Two Gram-stain-positive, aerobic, endospore-forming bacterial strains, isolated from the rhizosphere of
    MeSH term(s) Fatty Acids/chemistry ; Zea mays/microbiology ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Phylogeny ; Base Composition ; DNA, Bacterial/genetics ; Vitamin K 2 ; Bacterial Typing Techniques ; Paenibacillus
    Chemical Substances Fatty Acids ; RNA, Ribosomal, 16S ; DNA, Bacterial ; Vitamin K 2 (11032-49-8)
    Language English
    Publishing date 2023-04-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2002336-4
    ISSN 1466-5034 ; 1466-5026
    ISSN (online) 1466-5034
    ISSN 1466-5026
    DOI 10.1099/ijsem.0.005808
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences.

    Bigot, Thomas / Guglielmini, Julien / Criscuolo, Alexis

    Data in brief

    2019  Volume 25, Page(s) 104212

    Abstract: Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when ... ...

    Abstract Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when taking into account explicit evolutionary models. Data presented in this article are large sets of numbers of substitution events and associated numbers of observed differences between pairs of aligned amino acid sequences that have been generated through a simulation procedure of sequence evolution under a broad range of evolutionary models. These data are available at https://zenodo.org/record/2653704 (doi:10.5281/zenodo.2653704). They are accompanied in this paper by figures showing the strong relationship between the corresponding evolutionary and uncorrected distances, as well as estimated numerical constants that determine non-linear functions that fit the simulated data. These numerical constants can be useful to quickly estimate pairwise evolutionary distances directly from uncorrected distances between aligned amino acid sequences.
    Language English
    Publishing date 2019-07-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2019.104212
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences

    Bigot, Thomas / Guglielmini, Julien / Criscuolo, Alexis

    Data in Brief. 2019 Aug., v. 25

    2019  

    Abstract: Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when ... ...

    Abstract Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when taking into account explicit evolutionary models. Data presented in this article are large sets of numbers of substitution events and associated numbers of observed differences between pairs of aligned amino acid sequences that have been generated through a simulation procedure of sequence evolution under a broad range of evolutionary models. These data are available at https://zenodo.org/record/2653704 (doi:10.5281/zenodo.2653704). They are accompanied in this paper by figures showing the strong relationship between the corresponding evolutionary and uncorrected distances, as well as estimated numerical constants that determine non-linear functions that fit the simulated data. These numerical constants can be useful to quickly estimate pairwise evolutionary distances directly from uncorrected distances between aligned amino acid sequences.
    Keywords amino acids ; genomics ; phylogeny ; statistical analysis
    Language English
    Dates of publication 2019-08
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2019.104212
    Database NAL-Catalogue (AGRICOLA)

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