track cons11way
compositeTrack on
shortLabel Cactus 11-way
longLabel Cactus Alignment on 11 primate species
subGroup1 view Views align=Multiz_Alignments
dragAndDrop subTracks
visibility hide
type bed 4
group compGeno
html html/cactus11way

    track cons11wayViewalign
    shortLabel Multiz 11-way
    view align
    visibility pack
    viewUi on
    subTrack cons11way

        track cactus11way
        subTrack cons11wayViewalign
        shortLabel Cactus 11-way
        longLabel Cactus Alignment on 11 primate species
        subGroups view=align
        noInherit on
        type bigMaf
        viewUi on
        treeImage html/GCF_020740605.2_11way.png
        bigDataUrl bbi/GCF_020740605.2_mLemCat1.pri.cactus11way.bb
        summary bbi/GCF_020740605.2_mLemCat1.pri.cactus11waySummary.bb
        itemFirstCharCase noChange
        group compGeno
        color 0, 10, 100
        altColor 0,90,10
        speciesCodonDefault GCF_020740605.2
        speciesGroups Primates
        sGroup_Primates GCF_011100555 GCA_028878055 GCA_028885655 GCA_028885625 GCA_029281585 hs1 hg38 GCA_028858775 GCA_029289425 GCF_027406575
        speciesLabels GCF_020740605="ring-tailed lemur" hg38="human/GRCh38.p14" GCF_027406575="slow loris" GCA_029281585="western lowland gorilla" GCA_029289425="pygmy chimpanzee" GCA_028858775="chimpanzee" GCA_028885655="Sumatran orangutan" GCA_028885625="Bornean orangutan" hs1="T2T CHM13v2.0" GCF_011100555="white-tufted-ear marmoset" GCA_028878055="siamang"

# don't have irows yet
#        irows on
# don't have frames yet
#        frames bbi/GCF_020740605.2_mLemCat1.pri.cactus11wayFrames.bb

# row counts in summary.bed
# 570884 GCF_011100555.1
# 490137 GCA_028878055.2
# 487958 GCA_028885655.2
# 487921 GCA_028885625.2
# 486887 GCA_029281585.2
# 486484 hs1
# 485415 hg38
# 485144 GCA_028858775.2
# 484734 GCA_029289425.2
# 426725 GCF_027406575.1

# GCF_020740605.2_mLemCat1.pri ring-tailed lemur (mLemCat1 2021)
# GCF_027406575.1_mNycCou1.pri slow loris (primary hap 2022)
# GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri western lowland gorilla (v2 KB3781 2024)
# GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri pygmy chimpanzee (v2 primary hap 2024)
# GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri chimpanzee (v2 AG18354 primary hap 2024)
# GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri Sumatran orangutan (v2 AG06213 primary hap 2024)
# GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri Bornean orangutan (v2 AG05252 primary hap 2024)
# GCF_011100555.1_mCalJa1.2.pat.X white-tufted-ear marmoset (v1.2 2021 refseq)
# GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri siamang (v2 Jambi primary hap 2024)

track multiz11cons
compositeTrack on
shortLabel Multiz 11-way
longLabel Multiz Alignment on 11 primate species
subGroup1 view Views align=Multiz_Alignments
dragAndDrop subTracks
visibility hide
type bed 4
group compGeno
html html/multiz11way

    track multiz11wayViewalign
    shortLabel Multiz 11-way
    view align
    visibility pack
    viewUi on
    subTrack multiz11cons

        track multiz11way
        subTrack multiz11wayViewalign
        shortLabel Multiz 11-way
        longLabel Multiz Alignment on 11 primate species
        subGroups view=align
        noInherit on
        type bigMaf
        viewUi on
        treeImage html/GCF_020740605.2_11way.png
        bigDataUrl bbi/GCF_020740605.2_mLemCat1.pri.multiz11way.bb
        summary bbi/GCF_020740605.2_mLemCat1.pri.multiz11waySummary.bb
        itemFirstCharCase noChange
        group compGeno
        color 0, 10, 100
        altColor 0,90,10
        speciesCodonDefault GCF_020740605.2
        speciesGroups Primates
        sGroup_Primates GCF_011100555.1 GCA_028878055.2 GCA_028885655.2 GCA_028885625.2 GCA_029281585.2 hs1 hg38 GCA_028858775.2 GCA_029289425.2 GCF_027406575.1
        speciesLabels GCF_020740605.2="ring-tailed lemur" hg38="human/GRCh38.p14" GCF_027406575.1="slow loris" GCA_029281585.2="western lowland gorilla" GCA_029289425.2="pygmy chimpanzee" GCA_028858775.2="chimpanzee" GCA_028885655.2="Sumatran orangutan" GCA_028885625.2="Bornean orangutan" hs1="T2T CHM13v2.0" GCF_011100555.1="white-tufted-ear marmoset" GCA_028878055.2="siamang"

# don't have irows yet
#        irows on
# don't have frames yet
#        frames bbi/cactus11wayFrames.bb

# row counts in summary.bed
# 570884 GCF_011100555.1
# 490137 GCA_028878055.2
# 487958 GCA_028885655.2
# 487921 GCA_028885625.2
# 486887 GCA_029281585.2
# 486484 hs1
# 485415 hg38
# 485144 GCA_028858775.2
# 484734 GCA_029289425.2
# 426725 GCF_027406575.1

# GCF_020740605.2_mLemCat1.pri ring-tailed lemur (mLemCat1 2021)
# GCF_027406575.1_mNycCou1.pri slow loris (primary hap 2022)
# GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri western lowland gorilla (v2 KB3781 2024)
# GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri pygmy chimpanzee (v2 primary hap 2024)
# GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri chimpanzee (v2 AG18354 primary hap 2024)
# GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri Sumatran orangutan (v2 AG06213 primary hap 2024)
# GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri Bornean orangutan (v2 AG05252 primary hap 2024)
# GCF_011100555.1_mCalJa1.2.pat.X white-tufted-ear marmoset (v1.2 2021 refseq)
# GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri siamang (v2 Jambi primary hap 2024)