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/human/hg19/cons46way.html src/hg/makeDb/trackDb/human/hg19/cons46way.html
index 26474a48a30..0e5dc12986e 100644
--- src/hg/makeDb/trackDb/human/hg19/cons46way.html
+++ src/hg/makeDb/trackDb/human/hg19/cons46way.html
@@ -236,30 +236,32 @@
 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.
 Configuration buttons are available to select all of the species (<EM>Set 
 all</EM>), deselect all of the species (<EM>Clear all</EM>), or 
 use the default settings (<EM>Set defaults</EM>).
 By default, the following 11 species are included in the pairwise display:
 rhesus, mouse, dog, horse, 
 armadillo, opossum, platypus, lizard, 
 chicken, <EM>X. tropicalis</EM> (frog), and stickleback.
 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.</P>
 
 <H3>Gap Annotation</H3>