2ebbf76a87337459b3137c01283a4fa706538f14
braney
  Sat Mar 18 14:57:23 2023 -0700
turn on phylo logo on dev.   Turn off track download for squish
auxilliary tracks

diff --git src/hg/makeDb/trackDb/human/hg38/trackDb.100way.alpha.ra src/hg/makeDb/trackDb/human/hg38/trackDb.100way.alpha.ra
new file mode 100644
index 0000000..988cb38
--- /dev/null
+++ src/hg/makeDb/trackDb/human/hg38/trackDb.100way.alpha.ra
@@ -0,0 +1,114 @@
+track cons100way
+compositeTrack on
+shortLabel Conservation
+longLabel Vertebrate Multiz Alignment & Conservation (100 Species)
+subGroup1 view Views align=Multiz_Alignments  phyloP=Basewise_Conservation_(phyloP) phastcons=Element_Conservation_(phastCons) elements=Conserved_Elements 
+dragAndDrop subTracks
+visibility full
+type bed 4
+group compGeno
+priority 1
+
+    track cons100wayViewalign
+    shortLabel Multiz Alignments
+    view align
+    visibility pack
+    viewUi on
+    subTrack cons100way
+
+        track multiz100way
+        subTrack cons100wayViewalign on
+        shortLabel Multiz Align
+        longLabel Multiz Alignments of 100 Vertebrates
+        subGroups view=align
+        noInherit on
+        irows on
+        summary multiz100waySummary
+        frames multiz100wayFrames
+        group compGeno
+        color 0, 10, 100
+        altColor 0,90,10
+        type wigMaf 0.0 1.0
+        speciesCodonDefault hg38
+        speciesGroups Primate Euarchontoglires Laurasiatheria Afrotheria Mammal Birds Sarcopterygii Fish 
+        sGroup_Primate panTro4 gorGor3 ponAbe2 nomLeu3 rheMac3 macFas5 papAnu2 chlSab2 calJac3 saiBol1 otoGar3
+        sGroup_Euarchontoglires tupChi1 speTri2 jacJac1 micOch1 criGri1 mesAur1 mm10 rn6 hetGla2 cavPor3 chiLan1 octDeg1 oryCun2 ochPri3
+	sGroup_Laurasiatheria susScr3 vicPac2 camFer1 turTru2 orcOrc1 panHod1 bosTau8 oviAri3 capHir1 equCab2 cerSim1 felCat8 canFam3 musFur1 ailMel1 odoRosDiv1 lepWed1 pteAle1 pteVam1 myoDav1 myoLuc2 eptFus1 eriEur2 sorAra2 conCri1
+	sGroup_Afrotheria loxAfr3 eleEdw1 triMan1 chrAsi1 echTel2 oryAfe1
+	sGroup_Mammal dasNov3 monDom5 sarHar1 macEug2 ornAna1
+        sGroup_Birds falChe1 falPer1 ficAlb2 zonAlb1 geoFor1 taeGut2 pseHum1 melUnd1 amaVit1 araMac1 colLiv1 anaPla1 galGal4 melGal1
+        sGroup_Sarcopterygii allMis1 cheMyd1 chrPic2 pelSin1 apaSpi1 anoCar2 xenTro7 latCha1
+        sGroup_Fish tetNig2 fr3 takFla1 oreNil2 neoBri1 hapBur1 mayZeb1 punNye1 oryLat2 xipMac1 gasAcu1 gadMor1 danRer10 astMex1 lepOcu1 petMar2
+        speciesDefaultOff speTri2 micOch1 criGri1 mesAur1 rn6 hetGla2 cavPor3 chiLan1 octDeg1 oryCun2 ochPri3 susScr3 vicPac2 camFer1 turTru2 orcOrc1 panHod1 bosTau8 oviAri3 capHir1 equCab2 cerSim1 felCat8 musFur1 ailMel1 odoRosDiv1 lepWed1 pteAle1 pteVam1 myoDav1 myoLuc2 eptFus1 eriEur2 sorAra2 conCri1 eleEdw1 triMan1 chrAsi1 echTel2 oryAfe1 dasNov3 sarHar1 macEug2 ornAna1 falChe1 falPer1 ficAlb2 zonAlb1 geoFor1 taeGut2 pseHum1 melUnd1 amaVit1 araMac1 colLiv1 anaPla1 melGal1 allMis1 cheMyd1 chrPic2 pelSin1 apaSpi1 anoCar2 latCha1 tetNig2 fr3 takFla1 oreNil2 neoBri1 hapBur1 mayZeb1 punNye1 oryLat2 xipMac1 gasAcu1 gadMor1 astMex1 lepOcu1 calJac3 chlSab2 gorGor3 jacJac1 macFas5 monDom5 nomLeu3 otoGar3 panTro4 papAnu2 ponAbe2 saiBol1 tupChi1 petMar2
+        speciesDefaultOn hg38 canFam3 loxAfr3 xenTro7 danRer10 galGal4 rheMac3 mm10
+        defaultMaf multiz100wayDefault
+        itemFirstCharCase noChange
+        treeImage phylo/hg38_100way.png
+        priority 100
+
+    # PhyloP conservation
+    track cons100wayViewphyloP
+    shortLabel Basewise Conservation (phyloP)
+    view phyloP
+    visibility full
+    subTrack cons100way
+    viewLimits -20.0:9.869
+    viewLimitsMax -20:0.869
+
+        track phyloP100way
+        subTrack cons100wayViewphyloP on
+        subGroups view=phyloP
+        shortLabel Cons 100 Verts
+        longLabel 100 vertebrates Basewise Conservation by PhyloP
+        noInherit on
+        configurable on
+        type wig -20 7.532
+        maxHeightPixels 100:50:11
+        viewLimits -0.5:4
+        autoScale off
+        spanList 1
+        windowingFunction mean
+        color 60,60,140
+        altColor 140,60,60
+        priority 4
+        logoMaf multiz100way
+
+    # phastCons conservation
+    track cons100wayViewphastcons
+    shortLabel Element Conservation (phastCons)
+    view phastcons
+    visibility hide
+    subTrack cons100way
+
+        track phastCons100way
+        subTrack cons100wayViewphastcons off
+        subGroups view=phastcons
+        shortLabel Cons 100 Verts
+        longLabel 100 vertebrates conservation by PhastCons
+        noInherit on
+        configurable on
+        type wig 0 1
+        maxHeightPixels 100:40:11
+        autoScale off
+        spanList 1
+        windowingFunction mean
+        color 70,130,70
+        altColor 130,70,70
+        priority 13
+
+    # Conserved Elements (Most Conserved)
+    track cons100wayViewelements
+    shortLabel Conserved Elements
+    view elements
+    visibility hide
+    subTrack cons100way
+
+        track phastConsElements100way
+        subTrack cons100wayViewelements off
+        subGroups view=elements
+        shortLabel 100 Vert. El
+        longLabel 100 vertebrates Conserved Elements
+        noInherit on
+        color 110,10,40
+        type bed 5 .
+        priority 23