{
  "$schema": "https://jbrowse.org/jb2/schema/v5/config.json",
  "assemblies": [
    {
      "name": "RES",
      "displayName": "Rhopilema (jellyfish)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "RES-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "RES.chrom.sizes"
          }
        }
      }
    },
    {
      "name": "EMU",
      "displayName": "Ephydatia (sponge)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "EMU-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "EMU.chrom.sizes"
          }
        }
      }
    },
    {
      "name": "HCA",
      "displayName": "Hormiphora (comb jelly)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HCA-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HCA.chrom.sizes"
          }
        }
      }
    },
    {
      "name": "BIN",
      "displayName": "Bolinopsis (comb jelly)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "BIN-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "BIN.chrom.sizes"
          }
        }
      }
    },
    {
      "name": "BFL",
      "displayName": "Branchiostoma (amphioxus)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "BFL-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "BFL.chrom.sizes"
          }
        }
      }
    },
    {
      "name": "CLAa",
      "displayName": "Cladorhizid (sponge)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "CLAa-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "CLAa.chrom.sizes"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "SyntenyTrack",
      "trackId": "RES_EMU",
      "name": "RES vs EMU orthologs, colored by BCnS linkage group",
      "assemblyNames": ["RES", "EMU"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "uri": "RES_EMU.blocks.gz",
        "blockAssemblies": ["RES", "EMU"],
        "bedLocations": [
          {
            "uri": "RES_EMU.RES.bed.gz"
          },
          {
            "uri": "RES_EMU.EMU.bed.gz"
          }
        ],
        "attributeColumns": ["gene_group", "color", "break_FET"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "RES_HCA",
      "name": "RES vs HCA orthologs, colored by BCnS linkage group",
      "assemblyNames": ["RES", "HCA"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "uri": "RES_HCA.blocks.gz",
        "blockAssemblies": ["RES", "HCA"],
        "bedLocations": [
          {
            "uri": "RES_HCA.RES.bed.gz"
          },
          {
            "uri": "RES_HCA.HCA.bed.gz"
          }
        ],
        "attributeColumns": ["gene_group", "color", "break_FET"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "BIN_HCA",
      "name": "BIN vs HCA orthologs, colored by BCnS linkage group",
      "assemblyNames": ["BIN", "HCA"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "uri": "BIN_HCA.blocks.gz",
        "blockAssemblies": ["BIN", "HCA"],
        "bedLocations": [
          {
            "uri": "BIN_HCA.BIN.bed.gz"
          },
          {
            "uri": "BIN_HCA.HCA.bed.gz"
          }
        ],
        "attributeColumns": ["gene_group", "color", "break_FET"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "RES_BFL",
      "name": "RES vs BFL orthologs, colored by BCnS linkage group",
      "assemblyNames": ["RES", "BFL"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "uri": "RES_BFL.blocks.gz",
        "blockAssemblies": ["RES", "BFL"],
        "bedLocations": [
          {
            "uri": "RES_BFL.RES.bed.gz"
          },
          {
            "uri": "RES_BFL.BFL.bed.gz"
          }
        ],
        "attributeColumns": ["gene_group", "color", "break_FET"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "BFL_EMU",
      "name": "BFL vs EMU orthologs, colored by BCnS linkage group",
      "assemblyNames": ["BFL", "EMU"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "uri": "BFL_EMU.blocks.gz",
        "blockAssemblies": ["BFL", "EMU"],
        "bedLocations": [
          {
            "uri": "BFL_EMU.BFL.bed.gz"
          },
          {
            "uri": "BFL_EMU.EMU.bed.gz"
          }
        ],
        "attributeColumns": ["gene_group", "color", "break_FET"]
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "EMU_CLAa",
      "name": "EMU vs CLAa orthologs, colored by BCnS linkage group",
      "assemblyNames": ["EMU", "CLAa"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "uri": "EMU_CLAa.blocks.gz",
        "blockAssemblies": ["EMU", "CLAa"],
        "bedLocations": [
          {
            "uri": "EMU_CLAa.EMU.bed.gz"
          },
          {
            "uri": "EMU_CLAa.CLAa.bed.gz"
          }
        ],
        "attributeColumns": ["gene_group", "color", "break_FET"]
      }
    }
  ],
  "defaultSession": {
    "name": "Ancestral linkage groups",
    "views": [
      {
        "type": "DotplotView",
        "displayName": "Rhopilema (jellyfish) vs Ephydatia (sponge)",
        "views": [
          {
            "assembly": "RES"
          },
          {
            "assembly": "EMU",
            "displayedRegionNames": ["EMU*"]
          }
        ],
        "tracks": ["RES_EMU"],
        "encoding": { "color": "gene_group" },
        "autoDiagonalize": true,
        "lineWidth": 4,
        "height": 860
      }
    ]
  }
}