7a820a27de93e79180f99ae0e149585b5d1bb126
mspeir
  Tue Dec 23 16:02:10 2025 -0800
adding better species coloring description to rest of conservation tracks, refs #27217

diff --git src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
index 5cd1cd2a013..f8ac4cb1eaf 100644
--- src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
+++ src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
@@ -49,30 +49,32 @@
 The conservation wiggle 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.</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
 conventions are used:
 <UL>
 <LI><B>Single line:</B> No bases in the aligned species. Possibly due to a