Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Explain with AI

        Configure AI settings to get explanations of plots and data in this report.

        Keys entered here will be stored in your browser's local storage. See the docs.

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
        Settings are automatically saved. You can also save named configurations below.

        Save Settings

        You can save the toolbox settings for this report to the browser or as a file.

        Load Settings

        Choose a saved report profile from the browser or load from a file:

          Load from File

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.27

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/multiplesequencealign analysis pipeline. For information about how to interpret these results, please see the documentation.
        Application Type
        Muliple Sequence Alignment deplyoment and benchmarking.
        Report generated on 2025-04-30, 12:59 PDT based on data in: /gscratch/scrubbed/srlab/nxf.so092ISeRE

        Summary Stats

        Showing 6/6 rows and 10/22 columns.
        idfastatreeargs_treealignerargs_alignern_sequencesseqlength_meanseqlength_medianseqlength_maxperc_simsptcEVALUATEDAPDBiRMSDNiRMSDTCStotal_gapsavg_gapsplddtargs_tree_cleanargs_aligner_clean
        1
        seatoxin-ref
        DEFAULT
        MAFFT
        --dpparttree
        5
        47.0
        48.0
        49.0
        46.20%
        85.4
        57.1
        82.9
        74.8
        0.9
        1.1
        798.0
        35.0
        7.0
        0.8
        default
        --dpparttree
        2
        seatoxin-ref
        FAMSA
        FAMSA
        5
        47.0
        48.0
        49.0
        46.20%
        81.0
        46.9
        87.7
        76.2
        0.8
        0.9
        835.0
        20.0
        4.0
        0.8
        default
        default
        3
        seatoxin-ref
        DEFAULT
        CONSENSUS
        5
        47.0
        48.0
        49.0
        46.20%
        82.6
        51.0
        82.9
        74.5
        0.9
        1.1
        813.0
        30.0
        6.0
        0.8
        default
        default
        4
        toxin-ref
        DEFAULT
        MAFFT
        --dpparttree
        20
        63.5
        61.0
        74.0
        44.45%
        89.5
        51.9
        800.0
        330.0
        16.5
        default
        --dpparttree
        5
        toxin-ref
        FAMSA
        FAMSA
        20
        63.5
        61.0
        74.0
        44.45%
        89.3
        61.0
        802.0
        330.0
        16.5
        default
        default
        6
        toxin-ref
        DEFAULT
        CONSENSUS
        20
        63.5
        61.0
        74.0
        44.45%
        90.9
        64.9
        808.0
        330.0
        16.5
        default
        default

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        CALCULATE_SEQSTATSpython3.11.0
        CALC_GAPSawk1.3.4 20200120
        CONCAT_GAPScsvtk0.31.0
        CONCAT_PLDDTScsvtk0.31.0
        CONCAT_SEQSTATScsvtk0.31.0
        CONCAT_SIMSTATScsvtk0.31.0
        CONCAT_SPcsvtk0.31.0
        CONCAT_TCcsvtk0.31.0
        CONCAT_TCScsvtk0.31.0
        CONSENSUSpigz2.8)
        tcoffee13.46.0.919e8c6b
        EXTRACT_PLDDTawk1.3.4 20200120
        FAMSA_ALIGNfamsa2.2.2- (2022-10-09)
        FAMSA_GUIDETREEfamsa2.2.2- (2022-10-09)
        FASTAVALIDATORpy_fasta_validator0.6
        MAFFT_ALIGNmafft7.52
        pigz2.8)
        MERGE_EVALcsvtk0.31.0
        MERGE_STATScsvtk0.31.0
        MERGE_STATS_EVALcsvtk0.31.0
        PARSE_IRMSDpython3.11.0
        PARSE_SIMawk1.3.4 20200120
        cat8.32
        PIGZ_COMPRESSpigz2.8
        PREPARE_SHINYbash5.1.16 3
        TCOFFEE_ALNCOMPARE_SPpigz2.8)
        tcoffee13.46.0.919e8c6b
        TCOFFEE_ALNCOMPARE_TCpigz2.8)
        tcoffee13.46.0.919e8c6b
        TCOFFEE_EXTRACTFROMPDBtcoffee13.46.0.919e8c6b
        TCOFFEE_IRMSDpigz2.8)
        tcoffee13.46.0.919e8c6b
        TCOFFEE_SEQREFORMAT_SIMtcoffee13.46.0.919e8c6b
        TCOFFEE_TCSpigz2.8)
        tcoffee13.46.0.919e8c6b
        UNTARuntar1.34
        WorkflowNextflow24.10.5
        nf-core/multiplesequencealignv1.1.0-gde24fb1

        nf-core/multiplesequencealign Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/multiplesequencealign

        Methods

        Data was processed using nf-core/multiplesequencealign v1.1.0 (doi: 10.5281/zenodo.13889386) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.5 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/multiplesequencealign -profile test_tiny,conda -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config --outdir results

        Tools used in the workflow included: 3DCoffee (O'Sullivan et al., 2004) Biopython (Cock et al., 2009) Clustal Omega (Sievers et al., 2011) FAMSA (Deorowicz et al., 2016) FastQC (Andrews 2010), Foldmason (Gilchrist et al., 2024) Kalign 3 (Lassmann, 2019) learnMSA (Becker & Stanke, 2022) MAFFT (Katoh et al., 2002) MAGUS (Smirnov et al.,2021) mTM-align (Dong et al., 2018) MultiQC (Ewels et al., 2016) Muscle5 (Edgar, 2022) T-Coffee (Notredame et al., 2000) UPP (Park et al., 2023)

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
        • Becker F, Stanke M. learnMSA: learning and aligning large protein families. Gigascience. 2022 Nov 18;11:giac104. doi: 10.1093/gigascience/giac104. PMID: 36399060; PMCID: PMC9673500.
        • Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20. PMID: 19304878; PMCID: PMC2682512.
        • Deorowicz S, Debudaj-Grabysz A, Gudyś A. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Sci Rep. 2016 Sep 27;6:33964. doi: 10.1038/srep33964. PMID: 27670777; PMCID: PMC5037421.
        • Dong R, Peng Z, Zhang Y, Yang J. mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinformatics. 2018 May 15;34(10):1719-1725. doi: 10.1093/bioinformatics/btx828. PMID: 29281009; PMCID: PMC5946935.
        • Edgar RC. Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nat Commun. 2022 Nov 15;13(1):6968. doi: 10.1038/s41467-022-34630-w. PMID: 36379955; PMCID: PMC9664440.
        • Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
        • Cameron L.M. Gilchrist, Milot Mirdita, Martin Steinegger. bioRxiv 2024.08.01.606130; doi: https://doi.org/10.1101/2024.08.01.606130.
        • Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002 Jul 15;30(14):3059-66. doi: 10.1093/nar/gkf436. PMID: 12136088; PMCID: PMC135756.
        • Smirnov V, Warnow T. MAGUS: Multiple sequence Alignment using Graph clUStering. Bioinformatics. 2021 Jul 19;37(12):1666-1672. doi: 10.1093/bioinformatics/btaa992. PMID: 33252662; PMCID: PMC8289385.
        • Lassmann T. Kalign 3: multiple sequence alignment of large data sets. Bioinformatics. 2019 Oct 26;36(6):1928–9. doi: 10.1093/bioinformatics/btz795. Epub ahead of print. PMID: 31665271; PMCID: PMC7703769.
        • Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205-17. doi: 10.1006/jmbi.2000.4042. PMID: 10964570.
        • O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 2004 Jul 2;340(2):385-95. doi: 10.1016/j.jmb.2004.04.058. PMID: 15201059.
        • Park M, Ivanovic S, Chu G, Shen C, Warnow T. UPP2: fast and accurate alignment of datasets with fragmentary sequences. Bioinformatics. 2023 Jan 1;39(1):btad007. doi: 10.1093/bioinformatics/btad007. PMID: 36625535; PMCID: PMC9846425.
        • Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. PMID: 21988835; PMCID: PMC3261699.
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/multiplesequencealign Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/multiplesequencealign

        Basic Input/output options

        input
        https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/samplesheet/v1.1/samplesheet_test_af2.csv
        outdir
        results

        Tools input options

        tools
        https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/toolsheet/v1.1/toolsheet_tiny.csv

        Align options

        build_consensus
        true

        Stats options

        calc_seq_stats
        true
        calc_sim
        true
        extract_plddt
        true

        Eval options

        calc_irmsd
        true
        calc_tcs
        true

        Reports options

        shiny_app
        /mmfs1/home/strigg/.nextflow/assets/nf-core/multiplesequencealign/bin/shiny_app

        Institutional config options

        config_profile_contact
        Shelly A. Wanamaker @shellywanamaker
        config_profile_description
        UW Hyak Roberts labs cluster profile provided by nf-core/configs.
        config_profile_name
        Test profile
        config_profile_url
        https://faculty.washington.edu/sr320/

        Generic options

        trace_report_suffix
        2025-04-30_11-55-46

        Core Nextflow options

        configFiles
        /mmfs1/home/strigg/.nextflow/assets/nf-core/multiplesequencealign/nextflow.config, /gscratch/srlab/strigg/bin/uw_hyak_srlab.config
        containerEngine
        singularity
        launchDir
        /mmfs1/gscratch/scrubbed/strigg/analyses/20250430_Pmulti_MSA/tiny_test
        profile
        test_tiny,conda
        projectDir
        /mmfs1/home/strigg/.nextflow/assets/nf-core/multiplesequencealign
        revision
        master
        runName
        deadly_saha
        userName
        strigg
        workDir
        /mmfs1/gscratch/scrubbed/strigg/analyses/20250430_Pmulti_MSA/tiny_test/work

        MultiQC v1.27 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.