Data use in PlantGenIE


    Expression tools use TPM (Transcripts Per Kilobase Million) values for absolute expression, and no unit for the Row scaled or relative values. Absolute expression values were generated by aligning RNA-Seq reads to the reference genome and gene annotation with aligned read numbers then used to calculate TPM values.

    How we calculate the Relative Mean Difference (RMD)?

    Gene family construction settings


    Reference: Huson et al.

    • E-value threshold 1e-05
    • retaining the best 2500 hits


    Source: Official website

    • mclblastline
    • I = 2
    • scheme = 4
    • other parameters are left on their default values


    Source: Official website

    • Default settings, using DIAMOND output as input

    Phylogeny construction settings


    Source: Official website

    • default settings


    Source: Official website

    • Default settings


    Source: Official website

    • Default settings


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