3bcdba0cb7f7281dc131c2c59684980741a841e6
mspeir
  Tue Dec 23 15:34:36 2025 -0800
Adding better description of species coloring in conservation tracks, refs #27217

diff --git src/hg/makeDb/trackDb/mouse/mm10/cons60way.html src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
index ec7a64ddde9..8f1e9fe4dbc 100644
--- src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
+++ src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
@@ -151,30 +151,32 @@
 The conservation wiggles can be configured in a variety of ways to
 highlight different aspects of the displayed information.
 Click the <A HREF="../goldenPath/help/hgWiggleTrackHelp.html"
 TARGET=_blank>Graph configuration help</A> link for an explanation
 of the configuration options.</P>
 <P>
 Pairwise alignments of each species to the $organism genome are
 displayed below the conservation histogram as a grayscale density plot (in
 pack mode) or as a wiggle (in full mode) that indicates alignment quality.
 In dense display mode, conservation is shown in grayscale using
 darker values to indicate higher levels of overall conservation
 as scored by phastCons. </P>
 <P>
 Checkboxes on the track configuration page allow selection of the
 species to include in the pairwise display.
+The names of selected species are colored according to their clade,
+alternating between blue and green.
 Note that excluding species from the pairwise display does not alter the
 the conservation score display.</P>
 <P>
 To view detailed information about the alignments at a specific
 position, zoom the display in to 30,000 or fewer bases, then click on
 the alignment. For the Conserved Elements track, the name, or 'lod' of the items,
 signifies the raw output scores from phastCons. These scores were then transformed
 from 0-1000 for the score column of the track.
 See the methods section for more details.</P>
 
 <H3>Gap Annotation</H3>
 <P>
 The <EM>Display chains between alignments</EM> configuration option
 enables display of gaps between alignment blocks in the pairwise alignments in
 a manner similar to the Chain track display.  The following