1. SciScore for 10.1101/2022.01.12.475688: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    We used the GenBank MN908947.3 (RefSeq NC_045512.2) sequence as the reference for rooting the tree and used the sampling date metadata to derive from our comprehensive tree three subtrees containing the earliest 100K, 1M and 3M samples, referred to as 100K-sample tree, 1M-sample tree, and 3M-sample tree, respectively.
    RefSeq
    suggested: (RefSeq, RRID:SCR_003496)
    matOptimize also parallelizes Fitch-Sankoff computations for different loci and parsing of chunks of VCF using Intel’s TBB library (https://github.com/oneapi-src/oneTBB).
    matOptimize
    suggested: None
    Software Availability: The matOptimize code is available as part of the UShER package (https://github.com/yatisht/usher), which can also be installed via bioconda (https://bioconda.github.io/recipes/usher/README.html).
    UShER
    suggested: None

    Results from OddPub: Thank you for sharing your code.


    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.


    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


    Results from JetFighter: We did not find any issues relating to colormaps.


    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.


    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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