PDF Output

  1. Section I: ECM Overview
    • Top panel shows the predefined species tree.
    • Bottom panel shows the partition of input genes into Evolutionary Conserved Modules (ECMs), ordered by ECM strength (shown at right), and separated by horizontal lines.
    • Each row show one gene, where the phylogenetic profile indicates presence (blue) or absence (gray) of homologs in each species (column).
    • Gene symbols are shown at left. Gray color indicates that the gene is a paralog to a higher scoring gene within the same ECM (based on BLASTP E < 1e-3).
    • The next PDF section shows separate details for each ECM, where ECMs that contain two or more non-paralogous genes are indicated by an asterisk appended to the name (e.g. ECM2*).
  2. Section II: Details of each ECM and its expansion ECM+
    • Top panel shows the ECM’s inferred evolutionary history on the predefined species tree. Branch color indicates gene gain (blue), loss (red color, with brighter color indicating higher confidence in loss), or inheritance (black); otherwise branches are gray.
    • Bottom panel shows the input genes that are within the ECM (blue/white rows) as well as all genes in the expanded ECM+ (green/gray rows). The ECM+ includes genes likely to have arisen under the inferred model of evolution relative to a background model, and scored using a log likelihood ratio (LLR). Green color hue indicates LLR score.
    • PG indicates "paralog group" which are labeled alphabetically (i.e., A, B). The first gene within each paralog group is shown in black text. All other genes sharing sequence similarity (BLAST E < 1e-3) are assigned to the same PG label and displayed in gray text.