diff --git a/.gitignore b/.gitignore
index 4f52438..e9468e6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -81,3 +81,5 @@ Thumbs.db
 *.fa
 *.dat
 *.paml
+
+**/*.quarto_ipynb
diff --git a/Manifest.toml b/Manifest.toml
index 0116ad5..64a453c 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -1,8 +1,67 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.6"
+julia_version = "1.12.6"
 manifest_format = "2.0"
-project_hash = "d699c44afc5f926edeaca3ca751b2b16f5a17a39"
+project_hash = "94a4ec738340f4dda70b259df09e3bab55f07de4"
+
+[[deps.AbstractFFTs]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
+uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
+version = "1.5.0"
+
+    [deps.AbstractFFTs.extensions]
+    AbstractFFTsChainRulesCoreExt = "ChainRulesCore"
+    AbstractFFTsTestExt = "Test"
+
+    [deps.AbstractFFTs.weakdeps]
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[deps.AbstractTrees]]
+git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
+uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+version = "0.4.5"
+
+[[deps.Accessors]]
+deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"]
+git-tree-sha1 = "7063ad1083578215c7c4bf410368150abe8d5524"
+uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
+version = "0.1.45"
+
+    [deps.Accessors.extensions]
+    AxisKeysExt = "AxisKeys"
+    IntervalSetsExt = "IntervalSets"
+    LinearAlgebraExt = "LinearAlgebra"
+    StaticArraysExt = "StaticArrays"
+    StructArraysExt = "StructArrays"
+    TestExt = "Test"
+    UnitfulExt = "Unitful"
+
+    [deps.Accessors.weakdeps]
+    AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5"
+    IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+    StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+    StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
+[[deps.Adapt]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "daa72978cd7a624246e894a4f4f067706d4e17e2"
+uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+version = "4.7.0"
+weakdeps = ["SparseArrays", "StaticArrays"]
+
+    [deps.Adapt.extensions]
+    AdaptSparseArraysExt = "SparseArrays"
+    AdaptStaticArraysExt = "StaticArrays"
+
+[[deps.AdaptivePredicates]]
+git-tree-sha1 = "7e651ea8d262d2d74ce75fdf47c4d63c07dba7a6"
+uuid = "35492f91-a3bd-45ad-95db-fcad7dcfedb7"
+version = "1.2.0"
 
 [[deps.AliasTables]]
 deps = ["PtrArrays", "Random"]
@@ -10,6 +69,12 @@ git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff"
 uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8"
 version = "1.1.3"
 
+[[deps.Animations]]
+deps = ["Colors"]
+git-tree-sha1 = "e092fa223bf66a3c41f9c022bd074d916dc303e7"
+uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340"
+version = "0.4.2"
+
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 version = "1.1.2"
@@ -19,15 +84,32 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 version = "1.11.0"
 
 [[deps.Automa]]
-deps = ["PrecompileTools", "SIMD", "TranscodingStreams"]
-git-tree-sha1 = "a8f503e8e1a5f583fbef15a8440c8c7e32185df2"
+deps = ["PrecompileTools", "TranscodingStreams"]
+git-tree-sha1 = "94eab0b3ccdcac361188cc661daf69d4433c1818"
 uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
+version = "1.2.0"
+
+[[deps.AxisAlgorithms]]
+deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"]
+git-tree-sha1 = "01b8ccb13d68535d73d2b0c23e39bd23155fb712"
+uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950"
 version = "1.1.0"
 
+[[deps.AxisArrays]]
+deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"]
+git-tree-sha1 = "4126b08903b777c88edf1754288144a0492c05ad"
+uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
+version = "0.4.8"
+
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 version = "1.11.0"
 
+[[deps.BaseDirs]]
+git-tree-sha1 = "8c290a1b223deaeea9aea44b235d24546da8eb98"
+uuid = "18cc8868-cbac-4acf-b575-c8ff214dc66f"
+version = "1.4.0"
+
 [[deps.BioGenerics]]
 deps = ["TranscodingStreams"]
 git-tree-sha1 = "017562e86afcd2a6a2a9220606a40b54604887c9"
@@ -36,9 +118,9 @@ version = "0.1.5"
 
 [[deps.BioSequences]]
 deps = ["BioSymbols", "PrecompileTools", "Random", "Twiddle"]
-git-tree-sha1 = "3997810d996142e62aa426deed5bd858339e2332"
+git-tree-sha1 = "74bd40d3dfb74945a0fa40efcd073d5e3dc5a131"
 uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-version = "3.5.0"
+version = "3.5.1"
 
 [[deps.BioSymbols]]
 deps = ["PrecompileTools"]
@@ -46,38 +128,66 @@ git-tree-sha1 = "41e42d326ff01d12167f3f8a218b318bf7429d0f"
 uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
 version = "5.2.0"
 
+[[deps.Bzip2_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "1b96ea4a01afe0ea4090c5c8039690672dd13f2e"
+uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
+version = "1.0.9+0"
+
 [[deps.CEnum]]
 git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
 uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
 version = "0.5.0"
 
+[[deps.CRC32c]]
+uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc"
+version = "1.11.0"
+
+[[deps.CRlibm]]
+deps = ["CRlibm_jll"]
+git-tree-sha1 = "66188d9d103b92b6cd705214242e27f5737a1e5e"
+uuid = "96374032-68de-5a5b-8d9e-752f78720389"
+version = "1.0.2"
+
+[[deps.CRlibm_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "e329286945d0cfc04456972ea732551869af1cfc"
+uuid = "4e9b3aee-d8a1-5a3d-ad8b-7d824db253f0"
+version = "1.0.1+0"
+
 [[deps.CSV]]
 deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"]
-git-tree-sha1 = "deddd8725e5e1cc49ee205a1964256043720a6c3"
+git-tree-sha1 = "8d8e0b0f350b8e1c91420b5e64e5de774c2f0f4d"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.10.15"
-
-[[deps.CategoricalArrays]]
-deps = ["Compat", "DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"]
-git-tree-sha1 = "80ccd62b060efe8ff65d4edd4fa1ce9f653ae411"
-uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
-version = "1.0.1"
+version = "0.10.16"
+
+[[deps.Cairo]]
+deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"]
+git-tree-sha1 = "71aa551c5c33f1a4415867fe06b7844faadb0ae9"
+uuid = "159f3aea-2a34-519c-b102-8c37f9878175"
+version = "1.1.1"
+
+[[deps.CairoMakie]]
+deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"]
+git-tree-sha1 = "47142129b1777e21da58cff265050b10d8560588"
+uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+version = "0.15.13"
+
+[[deps.Cairo_jll]]
+deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
+git-tree-sha1 = "1fa950ebc3e37eccd51c6a8fe1f92f7d86263522"
+uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
+version = "1.18.7+0"
+
+[[deps.ChainRulesCore]]
+deps = ["Compat", "LinearAlgebra"]
+git-tree-sha1 = "12177ad6b3cad7fd50c8b3825ce24a99ad61c18f"
+uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+version = "1.26.1"
+weakdeps = ["SparseArrays"]
 
-    [deps.CategoricalArrays.extensions]
-    CategoricalArraysArrowExt = "Arrow"
-    CategoricalArraysJSONExt = "JSON"
-    CategoricalArraysRecipesBaseExt = "RecipesBase"
-    CategoricalArraysSentinelArraysExt = "SentinelArrays"
-    CategoricalArraysStatsBaseExt = "StatsBase"
-    CategoricalArraysStructTypesExt = "StructTypes"
-
-    [deps.CategoricalArrays.weakdeps]
-    Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"
-    JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-    SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-    StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-    StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
+    [deps.ChainRulesCore.extensions]
+    ChainRulesCoreSparseArraysExt = "SparseArrays"
 
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
@@ -85,16 +195,65 @@ git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9"
 uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
 version = "0.7.8"
 
+[[deps.CodecZstd]]
+deps = ["TranscodingStreams", "Zstd_jll"]
+git-tree-sha1 = "da54a6cd93c54950c15adf1d336cfd7d71f51a56"
+uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
+version = "0.8.7"
+
+[[deps.ColorBrewer]]
+deps = ["Colors", "JSON"]
+git-tree-sha1 = "07da79661b919001e6863b81fc572497daa58349"
+uuid = "a2cac450-b92f-5266-8821-25eda20663c8"
+version = "0.4.2"
+
+[[deps.ColorSchemes]]
+deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
+git-tree-sha1 = "b0fd3f56fa442f81e0a47815c92245acfaaa4e34"
+uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
+version = "3.31.0"
+
+[[deps.ColorTypes]]
+deps = ["FixedPointNumbers", "Random"]
+git-tree-sha1 = "67e11ee83a43eb71ddc950302c53bf33f0690dfe"
+uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
+version = "0.12.1"
+weakdeps = ["StyledStrings"]
+
+    [deps.ColorTypes.extensions]
+    StyledStringsExt = "StyledStrings"
+
+[[deps.ColorVectorSpace]]
+deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"]
+git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1"
+uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4"
+version = "0.11.0"
+weakdeps = ["SpecialFunctions"]
+
+    [deps.ColorVectorSpace.extensions]
+    SpecialFunctionsExt = "SpecialFunctions"
+
+[[deps.Colors]]
+deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
+git-tree-sha1 = "37ea44092930b1811e666c3bc38065d7d87fcc74"
+uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
+version = "0.13.1"
+
 [[deps.Combinatorics]]
-git-tree-sha1 = "8010b6bb3388abe68d95743dcbea77650bb2eddf"
+git-tree-sha1 = "c761b00e7755700f9cdf5b02039939d1359330e1"
 uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
-version = "1.0.3"
+version = "1.1.0"
+
+[[deps.CommonSolve]]
+git-tree-sha1 = "f54afab101687a7049833d07636418a83e9a250b"
+uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
+version = "0.2.12"
 
 [[deps.Compat]]
 deps = ["TOML", "UUIDs"]
-git-tree-sha1 = "0037835448781bb46feb39866934e243886d756a"
+git-tree-sha1 = "9d8a54ce4b17aa5bdce0ea5c34bc5e7c340d16ad"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.18.0"
+version = "4.18.1"
 weakdeps = ["Dates", "LinearAlgebra"]
 
     [deps.Compat.extensions]
@@ -103,33 +262,55 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.1.1+0"
+version = "1.3.0+1"
+
+[[deps.CompositionsBase]]
+git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad"
+uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b"
+version = "0.1.2"
+weakdeps = ["InverseFunctions"]
+
+    [deps.CompositionsBase.extensions]
+    CompositionsBaseInverseFunctionsExt = "InverseFunctions"
 
-[[deps.Conda]]
-deps = ["Downloads", "JSON", "VersionParsing"]
-git-tree-sha1 = "b19db3927f0db4151cb86d073689f2428e524576"
-uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-version = "1.10.2"
+[[deps.ComputePipeline]]
+deps = ["Observables", "Preferences"]
+git-tree-sha1 = "7bc84b769c1d384315e7b5c4ac03a6c303e6cf35"
+uuid = "95dc2771-c249-4cd0-9c9f-1f3b4330693c"
+version = "0.1.8"
 
 [[deps.ConstructionBase]]
 git-tree-sha1 = "b4b092499347b18a015186eae3042f72267106cb"
 uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 version = "1.6.0"
+weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"]
 
     [deps.ConstructionBase.extensions]
     ConstructionBaseIntervalSetsExt = "IntervalSets"
     ConstructionBaseLinearAlgebraExt = "LinearAlgebra"
     ConstructionBaseStaticArraysExt = "StaticArrays"
 
-    [deps.ConstructionBase.weakdeps]
-    IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
-    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-    StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+[[deps.Contour]]
+git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8"
+uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
+version = "0.6.3"
+
+[[deps.CoreMath]]
+deps = ["CoreMath_jll"]
+git-tree-sha1 = "8c0480f92b1b1796239156a1b9b1bfb1b39499b4"
+uuid = "b7a15901-be09-4a0e-87d2-2e66b0e09b5a"
+version = "0.1.0"
+
+[[deps.CoreMath_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "a692a4c1dc59a4b8bc0b6403876eb3250fde2bc3"
+uuid = "a38c48d9-6df1-5ac9-9223-b6ada3b5572b"
+version = "0.1.0+0"
 
 [[deps.Crayons]]
-git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
+git-tree-sha1 = "54b76cbb40d9a0f5368c880725b2f141da77c94f"
 uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
-version = "4.1.1"
+version = "4.2.0"
 
 [[deps.DataAPI]]
 git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
@@ -138,9 +319,9 @@ version = "1.16.0"
 
 [[deps.DataFrames]]
 deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6"
+git-tree-sha1 = "5fab31e2e01e70ad66e3e24c968c264d1cf166d6"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "1.7.0"
+version = "1.8.2"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -158,25 +339,33 @@ deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 version = "1.11.0"
 
+[[deps.DelaunayTriangulation]]
+deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "Random"]
+git-tree-sha1 = "c55f5a9fd67bdbc8e089b5a3111fe4292986a8e8"
+uuid = "927a84f5-c5f4-47a5-9785-b46e178433df"
+version = "1.6.6"
+
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 version = "1.11.0"
 
 [[deps.Distributions]]
-deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "3e6d038b77f22791b8e3472b7c633acea1ecac06"
+deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "Roots", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
+git-tree-sha1 = "d2facc77c08c1c2bfb1a77c148edd05b3db5410b"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.120"
+version = "0.25.130"
 
     [deps.Distributions.extensions]
     DistributionsChainRulesCoreExt = "ChainRulesCore"
     DistributionsDensityInterfaceExt = "DensityInterface"
+    DistributionsSparseConnectivityTracerExt = "SparseConnectivityTracer"
     DistributionsTestExt = "Test"
 
     [deps.Distributions.weakdeps]
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
     DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
+    SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
     Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.DocStringExtensions]]
@@ -187,7 +376,30 @@ version = "0.9.5"
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
-version = "1.6.0"
+version = "1.7.0"
+
+[[deps.EarCut_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053"
+uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5"
+version = "2.2.4+0"
+
+[[deps.EnumX]]
+git-tree-sha1 = "c49898e8438c828577f04b92fc9368c388ac783c"
+uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
+version = "1.0.7"
+
+[[deps.ExactPredicates]]
+deps = ["IntervalArithmetic", "Random", "StaticArrays"]
+git-tree-sha1 = "83231673ea4d3d6008ac74dc5079e77ab2209d8f"
+uuid = "429591f6-91af-11e9-00e2-59fbe8cec110"
+version = "2.2.9"
+
+[[deps.Expat_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "e6c4a6407a949e79a9d3f249bf49e6987c80e01f"
+uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
+version = "2.8.2+0"
 
 [[deps.FASTX]]
 deps = ["Automa", "BioGenerics", "PrecompileTools", "StringViews", "TranscodingStreams"]
@@ -199,6 +411,46 @@ weakdeps = ["BioSequences"]
     [deps.FASTX.extensions]
     BioSequencesExt = "BioSequences"
 
+[[deps.FFMPEG_jll]]
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libva_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
+git-tree-sha1 = "7a58e45171b63ed4782f2d36fdee8713a469e6e0"
+uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
+version = "8.1.2+0"
+
+[[deps.FFTA]]
+deps = ["AbstractFFTs", "DocStringExtensions", "LinearAlgebra", "MuladdMacro", "Primes", "Random", "Reexport"]
+git-tree-sha1 = "65e55303b72f4a567a51b174dd2c47496efeb95a"
+uuid = "b86e33f2-c0db-4aa1-a6e0-ab43e668529e"
+version = "0.3.1"
+
+[[deps.FileIO]]
+deps = ["Pkg", "Requires", "UUIDs"]
+git-tree-sha1 = "6621fef488e496356c9c9625d0562c12a6070819"
+uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+version = "1.20.0"
+
+    [deps.FileIO.extensions]
+    HTTPExt = "HTTP"
+
+    [deps.FileIO.weakdeps]
+    HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+
+[[deps.FilePaths]]
+deps = ["FilePathsBase", "MacroTools", "Reexport"]
+git-tree-sha1 = "a1b2fbfe98503f15b665ed45b3d149e5d8895e4c"
+uuid = "8fc22ac5-c921-52a6-82fd-178b2807b824"
+version = "0.9.0"
+
+    [deps.FilePaths.extensions]
+    FilePathsGlobExt = "Glob"
+    FilePathsURIParserExt = "URIParser"
+    FilePathsURIsExt = "URIs"
+
+    [deps.FilePaths.weakdeps]
+    Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+    URIParser = "30578b45-9adc-5946-b283-645ec420af67"
+    URIs = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
+
 [[deps.FilePathsBase]]
 deps = ["Compat", "Dates"]
 git-tree-sha1 = "3bab2c5aa25e7840a4b065805c0cdfc01f3068d2"
@@ -219,16 +471,58 @@ version = "1.11.0"
 
 [[deps.FillArrays]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a"
+git-tree-sha1 = "5bad39456d9f0166184fce2248783dd9862645c1"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "1.13.0"
-weakdeps = ["PDMats", "SparseArrays", "Statistics"]
+version = "1.17.0"
+weakdeps = ["PDMats", "SparseArrays", "StaticArrays", "Statistics"]
 
     [deps.FillArrays.extensions]
     FillArraysPDMatsExt = "PDMats"
     FillArraysSparseArraysExt = "SparseArrays"
+    FillArraysStaticArraysExt = "StaticArrays"
     FillArraysStatisticsExt = "Statistics"
 
+[[deps.FixedPointNumbers]]
+deps = ["Random", "Statistics"]
+git-tree-sha1 = "59af96b98217c6ef4ae0dfe065ac7c20831d1a84"
+uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
+version = "0.8.6"
+
+[[deps.Fontconfig_jll]]
+deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
+git-tree-sha1 = "f85dac9a96a01087df6e3a749840015a0ca3817d"
+uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
+version = "2.17.1+0"
+
+[[deps.Format]]
+git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc"
+uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
+version = "1.3.7"
+
+[[deps.FreeType]]
+deps = ["CEnum", "FreeType2_jll"]
+git-tree-sha1 = "907369da0f8e80728ab49c1c7e09327bf0d6d999"
+uuid = "b38be410-82b0-50bf-ab77-7b57e271db43"
+version = "4.1.1"
+
+[[deps.FreeType2_jll]]
+deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
+git-tree-sha1 = "70329abc09b886fd2c5d94ad2d9527639c421e3e"
+uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
+version = "2.14.3+1"
+
+[[deps.FreeTypeAbstraction]]
+deps = ["BaseDirs", "ColorVectorSpace", "Colors", "FreeType", "GeometryBasics", "Mmap"]
+git-tree-sha1 = "4ebb930ef4a43817991ba35db6317a05e59abd11"
+uuid = "663a7486-cb36-511b-a19d-713bb74d65c9"
+version = "0.10.8"
+
+[[deps.FriBidi_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "7a214fdac5ed5f59a22c2d9a885a16da1c74bbc7"
+uuid = "559328eb-81f9-559d-9380-de523a88c83c"
+version = "1.0.17+0"
+
 [[deps.Functors]]
 deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"]
 git-tree-sha1 = "60a0339f28a233601cb74468032b5c302d5067de"
@@ -241,21 +535,130 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 version = "1.11.0"
 
 [[deps.GLM]]
-deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"]
-git-tree-sha1 = "273bd1cd30768a2fddfa3fd63bbc746ed7249e5f"
+deps = ["Distributions", "LinearAlgebra", "LogExpFunctions", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsModels"]
+git-tree-sha1 = "c963639ae5b9aab54f543bdc7504f42f59880bec"
 uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
-version = "1.9.0"
+version = "1.9.5"
+
+[[deps.Gamma]]
+git-tree-sha1 = "86f86b6168a016ed88e4ae4e64577b98c3b59e8e"
+uuid = "a0844989-3bd2-4988-8bea-c9407ab0941b"
+version = "1.1.0"
+
+[[deps.GeometryBasics]]
+deps = ["EarCut_jll", "LinearAlgebra", "PrecompileTools", "Random", "StaticArrays"]
+git-tree-sha1 = "364685f5ffde25deb1bbcfd5bb278a5c6b7a9b37"
+uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
+version = "0.5.11"
+
+    [deps.GeometryBasics.extensions]
+    ExtentsExt = "Extents"
+    GeometryBasicsGeoInterfaceExt = "GeoInterface"
+    IntervalSetsExt = "IntervalSets"
+
+    [deps.GeometryBasics.weakdeps]
+    Extents = "411431e0-e8b7-467b-b5e0-f676ba4f2910"
+    GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
+    IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+
+[[deps.GettextRuntime_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll"]
+git-tree-sha1 = "45288942190db7c5f760f59c04495064eedf9340"
+uuid = "b0724c58-0f36-5564-988d-3bb0596ebc4a"
+version = "0.22.4+0"
+
+[[deps.Giflib_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "6570366d757b50fabae9f4315ad74d2e40c0560a"
+uuid = "59f7168a-df46-5410-90c8-f2779963d0ec"
+version = "5.2.3+0"
+
+[[deps.Glib_jll]]
+deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
+git-tree-sha1 = "090526e65de8f69648ac156daae153de8b56df62"
+uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
+version = "2.88.3+0"
+
+[[deps.Graphics]]
+deps = ["Colors", "LinearAlgebra", "NaNMath"]
+git-tree-sha1 = "a641238db938fff9b2f60d08ed9030387daf428c"
+uuid = "a2bd30eb-e257-5431-a919-1863eab51364"
+version = "1.1.3"
+
+[[deps.Graphite2_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "69ffb934a5c5b7e086a0b4fee3427db2556fba6e"
+uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472"
+version = "1.3.16+0"
+
+[[deps.GridLayoutBase]]
+deps = ["GeometryBasics", "InteractiveUtils", "Observables"]
+git-tree-sha1 = "93d5c27c8de51687a2c70ec0716e6e76f298416f"
+uuid = "3955a311-db13-416c-9275-1d80ed98e5e9"
+version = "0.11.2"
+
+[[deps.HarfBuzz_jll]]
+deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"]
+git-tree-sha1 = "f923f9a774fcf3f5cb761bfa43aeadd689714813"
+uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566"
+version = "8.5.1+0"
 
 [[deps.HypergeometricFunctions]]
-deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
-git-tree-sha1 = "68c173f4f449de5b438ee67ed0c9c748dc31a2ec"
+deps = ["Gamma", "LinearAlgebra"]
+git-tree-sha1 = "31bb6c92405c084617facc1d7ed9eb6c402d061e"
 uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
-version = "0.3.28"
+version = "0.3.30"
+
+[[deps.ImageAxes]]
+deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"]
+git-tree-sha1 = "e12629406c6c4442539436581041d372d69c55ba"
+uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac"
+version = "0.6.12"
+
+[[deps.ImageBase]]
+deps = ["ImageCore", "Reexport"]
+git-tree-sha1 = "eb49b82c172811fd2c86759fa0553a2221feb909"
+uuid = "c817782e-172a-44cc-b673-b171935fbb9e"
+version = "0.1.7"
+
+[[deps.ImageCore]]
+deps = ["ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"]
+git-tree-sha1 = "8c193230235bbcee22c8066b0374f63b5683c2d3"
+uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534"
+version = "0.10.5"
+
+[[deps.ImageIO]]
+deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs", "WebP"]
+git-tree-sha1 = "696144904b76e1ca433b886b4e7edd067d76cbf7"
+uuid = "82e4d734-157c-48bb-816b-45c225c6df19"
+version = "0.6.9"
+
+[[deps.ImageMetadata]]
+deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"]
+git-tree-sha1 = "2a81c3897be6fbcde0802a0ebe6796d0562f63ec"
+uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49"
+version = "0.9.10"
+
+[[deps.Imath_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "dcc8d0cd653e55213df9b75ebc6fe4a8d3254c65"
+uuid = "905a6f67-0a94-5f89-b386-d35d92009cd1"
+version = "3.2.2+0"
+
+[[deps.IndirectArrays]]
+git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f"
+uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959"
+version = "1.0.0"
+
+[[deps.Inflate]]
+git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d"
+uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9"
+version = "0.1.5"
 
 [[deps.InlineStrings]]
-git-tree-sha1 = "8594fac023c5ce1ef78260f24d1ad18b4327b420"
+git-tree-sha1 = "8f3d257792a522b4601c24a577954b0a8cd7334d"
 uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
-version = "1.4.4"
+version = "1.4.5"
 
     [deps.InlineStrings.extensions]
     ArrowTypesExt = "ArrowTypes"
@@ -265,20 +668,104 @@ version = "1.4.4"
     ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
     Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 
+[[deps.IntegerMathUtils]]
+git-tree-sha1 = "c72458f1962faeb003bf23cbdb75164fe6280906"
+uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235"
+version = "0.1.4"
+
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 version = "1.11.0"
 
+[[deps.Interpolations]]
+deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
+git-tree-sha1 = "48922d06068130f87e43edef52382e6a94305ae6"
+uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+version = "0.16.3"
+
+    [deps.Interpolations.extensions]
+    InterpolationsForwardDiffExt = "ForwardDiff"
+    InterpolationsUnitfulExt = "Unitful"
+
+    [deps.Interpolations.weakdeps]
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
+[[deps.IntervalArithmetic]]
+deps = ["CRlibm", "CoreMath", "MacroTools", "OpenBLASConsistentFPCSR_jll", "Printf", "Random", "RoundingEmulator"]
+git-tree-sha1 = "c3ee408ae340565f41699e3a3fa1053698c7626e"
+uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
+version = "1.0.10"
+
+    [deps.IntervalArithmetic.extensions]
+    IntervalArithmeticArblibExt = "Arblib"
+    IntervalArithmeticDiffRulesExt = "DiffRules"
+    IntervalArithmeticForwardDiffExt = "ForwardDiff"
+    IntervalArithmeticIntervalSetsExt = "IntervalSets"
+    IntervalArithmeticIrrationalConstantsExt = "IrrationalConstants"
+    IntervalArithmeticLinearAlgebraExt = "LinearAlgebra"
+    IntervalArithmeticRecipesBaseExt = "RecipesBase"
+    IntervalArithmeticSparseArraysExt = "SparseArrays"
+
+    [deps.IntervalArithmetic.weakdeps]
+    Arblib = "fb37089c-8514-4489-9461-98f9c8763369"
+    DiffRules = "b552c78f-8df3-52c6-915a-8e097449b14b"
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
+    IrrationalConstants = "92d709cd-6900-40b7-9082-c6be49f344b6"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[deps.IntervalSets]]
+git-tree-sha1 = "79d6bd28c8d9bccc2229784f1bd637689b256377"
+uuid = "8197267c-284f-5f27-9208-e0e47529a953"
+version = "0.7.14"
+
+    [deps.IntervalSets.extensions]
+    IntervalSetsRandomExt = "Random"
+    IntervalSetsRecipesBaseExt = "RecipesBase"
+    IntervalSetsStatisticsExt = "Statistics"
+
+    [deps.IntervalSets.weakdeps]
+    Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+    Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[deps.InverseFunctions]]
+git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb"
+uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
+version = "0.1.17"
+
+    [deps.InverseFunctions.extensions]
+    InverseFunctionsDatesExt = "Dates"
+    InverseFunctionsTestExt = "Test"
+
+    [deps.InverseFunctions.weakdeps]
+    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
 [[deps.InvertedIndices]]
 git-tree-sha1 = "6da3c4316095de0f5ee2ebd875df8721e7e0bdbe"
 uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
 version = "1.3.1"
 
 [[deps.IrrationalConstants]]
-git-tree-sha1 = "e2222959fbc6c19554dc15174c81bf7bf3aa691c"
+git-tree-sha1 = "b2d91fe939cae05960e760110b328288867b5758"
 uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
-version = "0.2.4"
+version = "0.2.6"
+
+[[deps.Isoband]]
+deps = ["isoband_jll"]
+git-tree-sha1 = "f9b6d97355599074dc867318950adaa6f9946137"
+uuid = "f1662d9f-8043-43de-a69a-05efc1cc6ff4"
+version = "0.1.1"
+
+[[deps.IterTools]]
+git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023"
+uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
+version = "1.10.0"
 
 [[deps.IteratorInterfaceExtensions]]
 git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
@@ -287,44 +774,142 @@ version = "1.0.0"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
-git-tree-sha1 = "0533e564aae234aff59ab625543145446d8b6ec2"
+git-tree-sha1 = "7204148362dafe5fe6a273f855b8ccbe4df8173e"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.7.1"
+version = "1.8.0"
 
 [[deps.JSON]]
-deps = ["Dates", "Mmap", "Parsers", "Unicode"]
-git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a"
+deps = ["Dates", "Logging", "Parsers", "PrecompileTools", "StructUtils", "UUIDs", "Unicode"]
+git-tree-sha1 = "c89d196f5ffb64bfbf80985b699ea913b0d2c211"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-version = "0.21.4"
+version = "1.6.1"
+
+    [deps.JSON.extensions]
+    JSONArrowExt = ["ArrowTypes"]
+
+    [deps.JSON.weakdeps]
+    ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
+
+[[deps.JpegTurbo]]
+deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"]
+git-tree-sha1 = "9496de8fb52c224a2e3f9ff403947674517317d9"
+uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0"
+version = "0.1.6"
+
+[[deps.JpegTurbo_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "1dae3057da6f2b9c857afef03177bbdc7c4afe92"
+uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
+version = "3.2.0+0"
+
+[[deps.JuliaSyntaxHighlighting]]
+deps = ["StyledStrings"]
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 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
@@ -342,15 +927,42 @@ version = "0.3.29"
     ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
     InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
 
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+
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+git-tree-sha1 = "f2c8715d05bf10f9d4dc354e69dee30b6be53239"
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+
+    [deps.Makie.extensions]
+    MakieDynamicQuantitiesExt = "DynamicQuantities"
+
+    [deps.Makie.weakdeps]
+    DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
+
+[[deps.MappedArrays]]
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+
 [[deps.Markdown]]
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+[[deps.MathTeXEngine]]
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 deps = ["DataAPI"]
@@ -362,9 +974,21 @@ version = "1.2.0"
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 version = "1.11.0"
 
+[[deps.MosaicViews]]
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+
 [[deps.MozillaCACerts_jll]]
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-version = "2023.12.12"
+version = "2025.11.4"
+
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 deps = ["CEnum", "NLopt_jll"]
@@ -380,23 +1004,78 @@ version = "1.2.1"
 
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-git-tree-sha1 = "b0154a615d5b2b6cf7a2501123b793577d0b9950"
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+
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+
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+    OffsetArraysAdaptExt = "Adapt"
+
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+
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+
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+
+[[deps.OpenSSL_jll]]
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 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"]
@@ -404,40 +1083,112 @@ git-tree-sha1 = "1346c9208249809840c91b26703912dff463d335"
 uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
 version = "0.5.6+0"
 
+[[deps.Opus_jll]]
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+
 [[deps.OrderedCollections]]
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+
+[[deps.PCRE2_jll]]
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+
+    [deps.PDMats.extensions]
+    StatsBaseExt = "StatsBase"
+
+[[deps.PNGFiles]]
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+
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+
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+
+[[deps.Pango_jll]]
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+git-tree-sha1 = "58e5ed5e386e156bd93e86b305ebd21ac63d2d04"
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-git-tree-sha1 = "7d2f8f21da5db6a806faf7b9b292296da42b2810"
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+
+[[deps.PhyloMakie]]
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+git-tree-sha1 = "c8bfe890934176d0a1c81c9e370da0a06a9e9b9b"
+repo-url = "git@github.com:jeetsukumaran/PhyloMakie.jl.git"
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 [[deps.PhyloNetworks]]
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-git-tree-sha1 = "1c73455735aa82eca2964d3e0b1b358827210038"
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-
-[[deps.PhyloPlots]]
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 [[deps.PhyloTraits]]
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-git-tree-sha1 = "48dee5627a6fb7877369b02f0ec50a431eeceedb"
+git-tree-sha1 = "a3e42f2cdffd598b1bd7e572794264fb869516c1"
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+version = "1.2.0"
+
+[[deps.Pixman_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"]
+git-tree-sha1 = "e4a6721aa89e62e5d4217c0b21bd714263779dda"
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+
+[[deps.Pkg]]
+deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+version = "1.12.1"
+weakdeps = ["REPL"]
+
+    [deps.Pkg.extensions]
+    REPLExt = "REPL"
+
+[[deps.PkgVersion]]
+deps = ["Pkg"]
+git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da"
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+
+[[deps.PlotUtils]]
+deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"]
+git-tree-sha1 = "26ca162858917496748aad52bb5d3be4d26a228a"
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+
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 [[deps.PooledArrays]]
 deps = ["DataAPI", "Future"]
@@ -447,37 +1198,63 @@ version = "1.4.3"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
-git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
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+version = "1.3.4"
 
 [[deps.Preferences]]
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-version = "1.4.3"
+version = "1.5.2"
 
 [[deps.PrettyTables]]
-deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
-git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34"
+deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "REPL", "Reexport", "StringManipulation", "Tables"]
+git-tree-sha1 = "988ff909479c5661b24f756432127198a7e465d0"
 uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "2.4.0"
+version = "3.4.3"
+
+    [deps.PrettyTables.extensions]
+    PrettyTablesExcelExt = "XLSX"
+    PrettyTablesTypstryExt = "Typstry"
+
+    [deps.PrettyTables.weakdeps]
+    Typstry = "f0ed7684-a786-439e-b1e3-3b82803b501e"
+    XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
+
+[[deps.Primes]]
+deps = ["IntegerMathUtils"]
+git-tree-sha1 = "25cdd1d20cd005b52fc12cb6be3f75faaf59bb9b"
+uuid = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae"
+version = "0.5.7"
 
 [[deps.Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 version = "1.11.0"
 
+[[deps.ProgressMeter]]
+deps = ["Distributed", "Printf"]
+git-tree-sha1 = "fbb92c6c56b34e1a2c4c36058f68f332bec840e7"
+uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
+version = "1.11.0"
+
 [[deps.PtrArrays]]
-git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d"
+git-tree-sha1 = "4fbbafbc6251b883f4d2705356f3641f3652a7fe"
 uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d"
-version = "1.3.0"
+version = "1.4.0"
+
+[[deps.QOI]]
+deps = ["ColorTypes", "FileIO", "FixedPointNumbers"]
+git-tree-sha1 = "472daaa816895cb7aee81658d4e7aec901fa1106"
+uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65"
+version = "1.0.2"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
-git-tree-sha1 = "9da16da70037ba9d701192e27befedefb91ec284"
+git-tree-sha1 = "5e8e8b0ab68215d7a2b14b9921a946fee794749e"
 uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-version = "2.11.2"
+version = "2.11.3"
 
     [deps.QuadGK.extensions]
     QuadGKEnzymeExt = "Enzyme"
@@ -485,20 +1262,8 @@ version = "2.11.2"
     [deps.QuadGK.weakdeps]
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 
-[[deps.RCall]]
-deps = ["CategoricalArrays", "Conda", "DataFrames", "DataStructures", "Dates", "Libdl", "Preferences", "REPL", "Random", "StatsModels", "WinReg"]
-git-tree-sha1 = "7521292e0ca900751cf0f35f2a2faf1cb321e960"
-uuid = "6f49c342-dc21-5d91-9882-a32aef131414"
-version = "0.14.9"
-
-    [deps.RCall.extensions]
-    RCallAxisArraysExt = ["AxisArrays"]
-
-    [deps.RCall.weakdeps]
-    AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
-
 [[deps.REPL]]
-deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"]
+deps = ["InteractiveUtils", "JuliaSyntaxHighlighting", "Markdown", "Sockets", "StyledStrings", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 version = "1.11.0"
 
@@ -507,11 +1272,32 @@ deps = ["SHA"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 version = "1.11.0"
 
+[[deps.RangeArrays]]
+git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5"
+uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d"
+version = "0.3.2"
+
+[[deps.Ratios]]
+deps = ["Requires"]
+git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b"
+uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439"
+version = "0.4.5"
+weakdeps = ["FixedPointNumbers"]
+
+    [deps.Ratios.extensions]
+    RatiosFixedPointNumbersExt = "FixedPointNumbers"
+
 [[deps.Reexport]]
 git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "1.2.2"
 
+[[deps.RelocatableFolders]]
+deps = ["SHA", "Scratch"]
+git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864"
+uuid = "05181044-ff0b-4ac5-8273-598c1e38db00"
+version = "1.0.1"
+
 [[deps.Requires]]
 deps = ["UUIDs"]
 git-tree-sha1 = "62389eeff14780bfe55195b7204c0d8738436d64"
@@ -520,9 +1306,9 @@ version = "1.3.1"
 
 [[deps.Rmath]]
 deps = ["Random", "Rmath_jll"]
-git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4"
+git-tree-sha1 = "5b3d50eb374cea306873b371d3f8d3915a018f0b"
 uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa"
-version = "0.8.0"
+version = "0.9.0"
 
 [[deps.Rmath_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -530,76 +1316,145 @@ git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8"
 uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
 version = "0.5.1+0"
 
+[[deps.Roots]]
+deps = ["Accessors", "CommonSolve", "Printf"]
+git-tree-sha1 = "7fb25a964849d90a0446366cdefca822e0e84900"
+uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
+version = "3.0.6"
+
+    [deps.Roots.extensions]
+    RootsChainRulesCoreExt = "ChainRulesCore"
+    RootsForwardDiffExt = "ForwardDiff"
+    RootsIntervalRootFindingExt = "IntervalRootFinding"
+    RootsSymPyExt = "SymPy"
+    RootsSymPyPythonCallExt = "SymPyPythonCall"
+    RootsUnitfulExt = "Unitful"
+
+    [deps.Roots.weakdeps]
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807"
+    SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6"
+    SymPyPythonCall = "bc8888f7-b21e-4b7c-a06a-5d9c9496438c"
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
+[[deps.RoundingEmulator]]
+git-tree-sha1 = "40b9edad2e5287e05bd413a38f61a8ff55b9557b"
+uuid = "5eaf0fd0-dfba-4ccb-bf02-d820a40db705"
+version = "0.2.1"
+
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 version = "0.7.0"
 
 [[deps.SIMD]]
 deps = ["PrecompileTools"]
-git-tree-sha1 = "fea870727142270bdf7624ad675901a1ee3b4c87"
+git-tree-sha1 = "e24dc23107d426a096d3eae6c165b921e74c18e4"
 uuid = "fdea26ae-647d-5447-a871-4b548cad5224"
-version = "3.7.1"
+version = "3.7.2"
+
+[[deps.Scratch]]
+deps = ["Dates"]
+git-tree-sha1 = "9b81b8393e50b7d4e6d0a9f14e192294d3b7c109"
+uuid = "6c6a2e73-6563-6170-7368-637461726353"
+version = "1.3.0"
 
 [[deps.SentinelArrays]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "712fb0231ee6f9120e005ccd56297abbc053e7e0"
+git-tree-sha1 = "084c47c7c5ce5cfecefa0a98dff69eb3646b5a80"
 uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-version = "1.4.8"
+version = "1.4.10"
 
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 version = "1.11.0"
 
+[[deps.ShaderAbstractions]]
+deps = ["ColorTypes", "FixedPointNumbers", "GeometryBasics", "LinearAlgebra", "Observables", "StaticArrays"]
+git-tree-sha1 = "818554664a2e01fc3784becb2eb3a82326a604b6"
+uuid = "65257c39-d410-5151-9873-9b3e5be5013e"
+version = "0.5.0"
+
+[[deps.SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+version = "1.11.0"
+
 [[deps.ShiftedArrays]]
 git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16"
 uuid = "1277b4bf-5013-50f5-be3d-901d8477a67a"
 version = "2.0.0"
 
+[[deps.SignedDistanceFields]]
+deps = ["Statistics"]
+git-tree-sha1 = "3949ad92e1c9d2ff0cd4a1317d5ecbba682f4b92"
+uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96"
+version = "0.4.1"
+
+[[deps.SimpleTraits]]
+deps = ["InteractiveUtils", "MacroTools"]
+git-tree-sha1 = "7ddb0b49c109481b046972c0e4ab02b2127d6a75"
+uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
+version = "0.9.6"
+
+[[deps.Sixel]]
+deps = ["Dates", "FileIO", "ImageCore", "IndirectArrays", "OffsetArrays", "REPL", "libsixel_jll"]
+git-tree-sha1 = "0494aed9501e7fb65daba895fb7fd57cc38bc743"
+uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47"
+version = "0.1.5"
+
 [[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 version = "1.11.0"
 
 [[deps.SortingAlgorithms]]
 deps = ["DataStructures"]
-git-tree-sha1 = "64d974c2e6fdf07f8155b5b2ca2ffa9069b608d9"
+git-tree-sha1 = "13cd91cc9be159e3f4d95b857fa2aa383b53772a"
 uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
-version = "1.2.2"
+version = "1.2.3"
 
 [[deps.SparseArrays]]
 deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-version = "1.11.0"
+version = "1.12.0"
 
 [[deps.SpecialFunctions]]
 deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "41852b8679f78c8d8961eeadc8f62cef861a52e3"
+git-tree-sha1 = "6547cbdd8ce32efba0d21c5a40fa96d1a3548f9f"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "2.5.1"
+version = "2.8.0"
+weakdeps = ["ChainRulesCore"]
 
     [deps.SpecialFunctions.extensions]
     SpecialFunctionsChainRulesCoreExt = "ChainRulesCore"
 
-    [deps.SpecialFunctions.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+[[deps.StableRNGs]]
+deps = ["Random"]
+git-tree-sha1 = "4f96c596b8c8258cc7d3b19797854d368f243ddc"
+uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
+version = "1.0.4"
+
+[[deps.StackViews]]
+deps = ["OffsetArrays"]
+git-tree-sha1 = "be1cf4eb0ac528d96f5115b4ed80c26a8d8ae621"
+uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15"
+version = "0.1.2"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "cbea8a6bd7bed51b1619658dec70035e07b8502f"
+git-tree-sha1 = "246a8bb2e6667f832eea063c3a56aef96429a3db"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.14"
+version = "1.9.18"
+weakdeps = ["ChainRulesCore", "Statistics"]
 
     [deps.StaticArrays.extensions]
     StaticArraysChainRulesCoreExt = "ChainRulesCore"
     StaticArraysStatisticsExt = "Statistics"
 
-    [deps.StaticArrays.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-    Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-
 [[deps.StaticArraysCore]]
-git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682"
+git-tree-sha1 = "6ab403037779dae8c514bad259f32a447262455a"
 uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
-version = "1.4.3"
+version = "1.4.4"
 
 [[deps.Statistics]]
 deps = ["LinearAlgebra"]
@@ -613,46 +1468,80 @@ weakdeps = ["SparseArrays"]
 
 [[deps.StatsAPI]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "9d72a13a3f4dd3795a195ac5a44d7d6ff5f552ff"
+git-tree-sha1 = "178ed29fd5b2a2cfc3bd31c13375ae925623ff36"
 uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
-version = "1.7.1"
+version = "1.8.0"
 
 [[deps.StatsBase]]
-deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "2c962245732371acd51700dbb268af311bddd719"
+deps = ["AliasTables", "DataAPI", "DataStructures", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
+git-tree-sha1 = "e4d7a1a0edc20af42689ea6f4f3587a2175d50ee"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.34.6"
+version = "0.34.12"
 
 [[deps.StatsFuns]]
 deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "8e45cecc66f3b42633b8ce14d431e8e57a3e242e"
+git-tree-sha1 = "91f091a8716a6bb38417a6e6f274602a19aaa685"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "1.5.0"
+version = "1.5.2"
+weakdeps = ["ChainRulesCore", "InverseFunctions"]
 
     [deps.StatsFuns.extensions]
     StatsFunsChainRulesCoreExt = "ChainRulesCore"
     StatsFunsInverseFunctionsExt = "InverseFunctions"
 
-    [deps.StatsFuns.weakdeps]
-    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-    InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
-
 [[deps.StatsModels]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"]
-git-tree-sha1 = "728d276a5adc2f1cbb800eec4b63d0a8221024b4"
+git-tree-sha1 = "0db41c4e0d9f3fa195395a6401a8290752c9cd3d"
 uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
-version = "0.7.5"
+version = "0.7.10"
 
 [[deps.StringManipulation]]
 deps = ["PrecompileTools"]
-git-tree-sha1 = "725421ae8e530ec29bcbdddbe91ff8053421d023"
+git-tree-sha1 = "8a90c1d77c3277a5d43b83927b3cbe2c70a37484"
 uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
-version = "0.4.1"
+version = "0.4.7"
 
 [[deps.StringViews]]
-git-tree-sha1 = "d3c7a06c80622b8404b1105886c732abcb25cc2b"
+git-tree-sha1 = "f2dcb92855b31ad92fe8f079d4f75ac57c93e4b8"
 uuid = "354b36f9-a18e-4713-926e-db85100087ba"
-version = "1.3.5"
+version = "1.3.7"
+
+[[deps.StructArrays]]
+deps = ["ConstructionBase", "DataAPI", "Tables"]
+git-tree-sha1 = "ad8002667372439f2e3611cfd14097e03fa4bccd"
+uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+version = "0.7.3"
+
+    [deps.StructArrays.extensions]
+    StructArraysAdaptExt = "Adapt"
+    StructArraysGPUArraysCoreExt = ["GPUArraysCore", "KernelAbstractions"]
+    StructArraysLinearAlgebraExt = "LinearAlgebra"
+    StructArraysSparseArraysExt = "SparseArrays"
+    StructArraysStaticArraysExt = "StaticArrays"
+
+    [deps.StructArrays.weakdeps]
+    Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+    GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
+    KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+    StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+
+[[deps.StructUtils]]
+deps = ["Dates", "UUIDs"]
+git-tree-sha1 = "82bee338d650aa515f31866c460cb7e3bcef90b8"
+uuid = "ec057cc2-7a8d-4b58-b3b3-92acb9f63b42"
+version = "2.8.2"
+
+    [deps.StructUtils.extensions]
+    StructUtilsMeasurementsExt = ["Measurements"]
+    StructUtilsStaticArraysCoreExt = ["StaticArraysCore"]
+    StructUtilsTablesExt = ["Tables"]
+
+    [deps.StructUtils.weakdeps]
+    Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
+    StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
+    Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [[deps.StyledStrings]]
 uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b"
@@ -665,7 +1554,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 [[deps.SuiteSparse_jll]]
 deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
-version = "7.7.0+0"
+version = "7.8.3+2"
 
 [[deps.TOML]]
 deps = ["Dates"]
@@ -680,15 +1569,37 @@ version = "1.0.1"
 
 [[deps.Tables]]
 deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"]
-git-tree-sha1 = "f2c1efbc8f3a609aadf318094f8fc5204bdaf344"
+git-tree-sha1 = "0f38a06c83f0007bbab3cf911262841c9a0f07e0"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "1.12.1"
+version = "1.13.0"
+
+[[deps.Tar]]
+deps = ["ArgTools", "SHA"]
+uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+version = "1.10.0"
+
+[[deps.TensorCore]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6"
+uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50"
+version = "0.1.1"
+
+[[deps.TiffImages]]
+deps = ["CodecZstd", "ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "PrecompileTools", "ProgressMeter", "SIMD", "UUIDs"]
+git-tree-sha1 = "9ca5f1f2d42f80df4b8c9f6ab5a64f438bbd9976"
+uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
+version = "0.11.9"
 
 [[deps.TranscodingStreams]]
 git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.11.3"
 
+[[deps.TriplotBase]]
+git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b"
+uuid = "981d1d27-644d-49a2-9326-4793e63143c3"
+version = "0.1.0"
+
 [[deps.Twiddle]]
 git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a"
 uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
@@ -703,38 +1614,212 @@ version = "1.11.0"
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 version = "1.11.0"
 
-[[deps.VersionParsing]]
-git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868"
-uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
-version = "1.3.0"
+[[deps.UnicodeFun]]
+deps = ["REPL"]
+git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf"
+uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1"
+version = "0.4.1"
+
+[[deps.Unitful]]
+deps = ["Dates", "LinearAlgebra", "Random"]
+git-tree-sha1 = "57e1b2c9de4bd6f40ecb9de4ac1797b81970d008"
+uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
+version = "1.28.0"
+
+    [deps.Unitful.extensions]
+    ConstructionBaseUnitfulExt = "ConstructionBase"
+    ForwardDiffExt = "ForwardDiff"
+    InverseFunctionsUnitfulExt = "InverseFunctions"
+    LatexifyExt = ["Latexify", "LaTeXStrings"]
+    NaNMathExt = "NaNMath"
+    PrintfExt = "Printf"
+
+    [deps.Unitful.weakdeps]
+    ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
+    LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
+    Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+    NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
+    Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [[deps.WeakRefStrings]]
 deps = ["DataAPI", "InlineStrings", "Parsers"]
-git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23"
+git-tree-sha1 = "0716e01c3b40413de5dedbc9c5c69f27cddfddfc"
 uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
-version = "1.4.2"
+version = "1.4.3"
 
-[[deps.WinReg]]
-git-tree-sha1 = "cd910906b099402bcc50b3eafa9634244e5ec83b"
-uuid = "1b915085-20d7-51cf-bf83-8f477d6f5128"
-version = "1.0.0"
+[[deps.WebP]]
+deps = ["CEnum", "ColorTypes", "FileIO", "FixedPointNumbers", "ImageCore", "libwebp_jll"]
+git-tree-sha1 = "aa1ca3c47f119fbdae8770c29820e5e6119b83f2"
+uuid = "e3aaa7dc-3e4b-44e0-be63-ffb868ccd7c1"
+version = "0.1.3"
+
+[[deps.WoodburyMatrices]]
+deps = ["LinearAlgebra", "SparseArrays"]
+git-tree-sha1 = "248a7031b3da79a127f14e5dc5f417e26f9f6db7"
+uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
+version = "1.1.0"
 
 [[deps.WorkerUtilities]]
 git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7"
 uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60"
 version = "1.6.1"
 
+[[deps.XZ_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "b29c22e245d092b8b4e8d3c09ad7baa586d9f573"
+uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
+version = "5.8.3+0"
+
+[[deps.Xorg_libX11_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
+git-tree-sha1 = "808090ede1d41644447dd5cbafced4731c56bd2f"
+uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc"
+version = "1.8.13+0"
+
+[[deps.Xorg_libXau_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "aa1261ebbac3ccc8d16558ae6799524c450ed16b"
+uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec"
+version = "1.0.13+0"
+
+[[deps.Xorg_libXdmcp_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "52858d64353db33a56e13c341d7bf44cd0d7b309"
+uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05"
+version = "1.1.6+0"
+
+[[deps.Xorg_libXext_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
+git-tree-sha1 = "1a4a26870bf1e5d26cd585e38038d399d7e65706"
+uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3"
+version = "1.3.8+0"
+
+[[deps.Xorg_libXfixes_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
+git-tree-sha1 = "75e00946e43621e09d431d9b95818ee751e6b2ef"
+uuid = "d091e8ba-531a-589c-9de9-94069b037ed8"
+version = "6.0.2+0"
+
+[[deps.Xorg_libXrender_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
+git-tree-sha1 = "7ed9347888fac59a618302ee38216dd0379c480d"
+uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa"
+version = "0.9.12+0"
+
+[[deps.Xorg_libpciaccess_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
+git-tree-sha1 = "58972370b81423fc546c56a60ed1a009450177c3"
+uuid = "a65dc6b1-eb27-53a1-bb3e-dea574b5389e"
+version = "0.19.0+0"
+
+[[deps.Xorg_libxcb_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXau_jll", "Xorg_libXdmcp_jll"]
+git-tree-sha1 = "bfcaf7ec088eaba362093393fe11aa141fa15422"
+uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b"
+version = "1.17.1+0"
+
+[[deps.Xorg_xtrans_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "a63799ff68005991f9d9491b6e95bd3478d783cb"
+uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10"
+version = "1.6.0+0"
+
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.13+1"
+version = "1.3.1+2"
+
+[[deps.Zstd_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "446b23e73536f84e8037f5dce465e92275f6a308"
+uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
+version = "1.5.7+1"
+
+[[deps.isoband_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c"
+uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4"
+version = "0.2.3+0"
+
+[[deps.libaom_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "850b06095ee71f0135d644ffd8a52850699581ed"
+uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b"
+version = "3.13.3+0"
+
+[[deps.libass_jll]]
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
+git-tree-sha1 = "125eedcb0a4a0bba65b657251ce1d27c8714e9d6"
+uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
+version = "0.17.4+0"
 
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.11.0+0"
+version = "5.15.0+0"
+
+[[deps.libdrm_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libpciaccess_jll"]
+git-tree-sha1 = "28e57478e8a160d346a19c28b3fffb9273bcc9c2"
+uuid = "8e53e030-5e6c-5a89-a30b-be5b7263a166"
+version = "2.4.134+0"
+
+[[deps.libfdk_aac_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "646634dd19587a56ee2f1199563ec056c5f228df"
+uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280"
+version = "2.0.4+0"
+
+[[deps.libpng_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
+git-tree-sha1 = "e51150d5ab85cee6fc36726850f0e627ad2e4aba"
+uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
+version = "1.6.58+0"
+
+[[deps.libsixel_jll]]
+deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "libpng_jll"]
+git-tree-sha1 = "c1733e347283df07689d71d61e14be986e49e47a"
+uuid = "075b6546-f08a-558a-be8f-8157d0f608a5"
+version = "1.10.5+0"
+
+[[deps.libva_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll", "Xorg_libXfixes_jll", "libdrm_jll"]
+git-tree-sha1 = "7dbf96baae3310fe2fa0df0ccbb3c6288d5816c9"
+uuid = "9a156e7d-b971-5f62-b2c9-67348b8fb97c"
+version = "2.23.0+0"
+
+[[deps.libvorbis_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll"]
+git-tree-sha1 = "11e1772e7f3cc987e9d3de991dd4f6b2602663a5"
+uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
+version = "1.3.8+0"
+
+[[deps.libwebp_jll]]
+deps = ["Artifacts", "Giflib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libglvnd_jll", "Libtiff_jll", "libpng_jll"]
+git-tree-sha1 = "4e4282c4d846e11dce56d74fa8040130b7a95cb3"
+uuid = "c5f90fcd-3b7e-5836-afba-fc50a0988cb2"
+version = "1.6.0+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
-version = "1.59.0+0"
+version = "1.64.0+1"
+
+[[deps.p7zip_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
+uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
+version = "17.7.0+0"
+
+[[deps.x264_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "14cc7083fc6dff3cc44f2bc435ee96d06ed79aa7"
+uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
+version = "10164.0.1+0"
+
+[[deps.x265_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "e7b67590c14d487e734dcb925924c5dc43ec85f3"
+uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
+version = "4.1.0+0"
diff --git a/Project.toml b/Project.toml
index e693eb7..c554ad3 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,12 +1,14 @@
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+PhyloMakie = "ccbd7354-87c9-452d-961c-17247803ee9f"
 PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
-PhyloPlots = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
 PhyloTraits = "bce24f4f-6725-4ba4-a77f-2b043c8e33c5"
-RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
+
+[sources]
+PhyloMakie = {url = "git@github.com:jeetsukumaran/PhyloMakie.jl.git"}
\ No newline at end of file
diff --git a/_quarto.yml b/_quarto.yml
index d0b214f..e760041 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -46,5 +46,9 @@ format:
     css: styles.css
     toc: true
 
-# engines: ['julia'] # problem: due to each Rcall to R in a separate environment
-jupyter: julia-1.11  # older engine. solves the problem. installation more complex
+# No RCall/R dependency remains, so the old "each Rcall call needs its own
+# environment" reason for pinning the jupyter engine is gone. The native
+# `engine: julia` project setting was tried and did not render reliably in
+# testing, so this still uses the jupyter engine with an IJulia kernel;
+# match the kernel name below to whatever `julia -v` reports on your machine.
+jupyter: julia-1.12
diff --git a/readme.md b/readme.md
index c0b1412..87290f3 100644
--- a/readme.md
+++ b/readme.md
@@ -7,9 +7,9 @@ This repository contains materials for a tutorial.
   [PhyloNetworks](https://github.com/juliaphylo/PhyloNetworks.jl),
   [PhyloTraits](https://github.com/juliaphylo/PhyloTraits.jl),
   and visualized with
-  [PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl).  
+  [PhyloMakie](https://github.com/jeetsukumaran/PhyloMakie.jl).
   It was tested with julia v1.11, PhyloNetworks v1.1.0,
-  PhyloTraits v1.1.0 and PhyloPlots v2.1.0.
+  PhyloTraits v1.1.0 and PhyloMakie v0.1.0.
 
 The website was rendered with
 [quarto](https://quarto.org/docs/websites/) v1.7.33,
diff --git a/topic1-installation.qmd b/topic1-installation.qmd
index c75582c..d7e90d7 100644
--- a/topic1-installation.qmd
+++ b/topic1-installation.qmd
@@ -11,7 +11,6 @@ Here are steps to get ready for the tutorial.
   and add it to your [`PATH`](https://julialang.org/downloads/platform/#optional_add_julia_to_path)
 - install [VSCode](https://code.visualstudio.com/download)
   or another editor, if you don't have one already.
-- install [R](https://cran.r-project.org)
 
 ### customize VSCode
 
@@ -58,14 +57,12 @@ The code is in files named like `topic*.qmd`.
 
 ### install packages
 
-Open julia, e.g. in a terminal integrated in VSCode. Preferably, open julia
-from the tutorial directory (cloned or downloaded earlier)
-to make it easier to use this directory as a julia environment.
+Your active Julia environment will need the following packages available:
+
+- the core [PhyloNetworks](https://juliaphylo.github.io/PhyloNetworks.jl/stable/man/installation/),
+- [PhyloMakie](https://github.com/jeetsukumaran/PhyloMakie.jl) for plotting networks, and
+- [CairoMakie](https://docs.makie.org/stable/explanations/backends/cairomakie/) as the Makie backend used to render static figures.
 
-Then within julia, install
-[PhyloNetworks](https://juliaphylo.github.io/PhyloNetworks.jl/stable/man/installation/).
-Also install other packages, including:
-[PhyloPlots](https://juliaphylo.github.io/PhyloPlots.jl/stable/man/installation/#Installation).
 For this, we suggest using the environment provided in this tutorial,
 which consists of the two `.toml` files that lists which packages to install
 (in `Project.toml`) and which versions exactly (in `Manifest.toml`).
@@ -75,6 +72,7 @@ and will install the exact versions of the packages used while writing this tuto
 of the GitHub repository).
 Here is how:
 
+- Open julia, e.g. in a terminal integrated in VSCode from  the tutorial directory (cloned or downloaded earlier)
 - type `]` to switch to package mode
 - type `activate .` if your current directory is the tutorial folder.
   Otherwise, type `activate path-to-tutorial-folder` to activate
@@ -84,28 +82,29 @@ Here is how:
   files. It will pre-compile them for the environment, in a way that won't
   interfere with other julia environments (if any).
 
-Alternatively, if you want to install these packages in the default or any
-other environment, type `]` to switch to package mode. Julia will show a prompt
-like this: `(networkPCM-tutorial) pkg>` showing the name of the folder used
-as environment, followed by "pkg>" to mean that it's in package mode.
-Then type this:
+Alternatively, if you want to install these packages in the global environment, activated by launching Julia directly without a `--project` flag:
+
+
+```bash
+julia
+```
+
+or some other specific environment of your choice, e.g.
+
+```bash
+cd projects/computing/learning/network-pcm
+julia --project=. 
+```
+and then run the following commands: 
+
 ```julia
-add CSV, CategoricalArrays, DataFrames
-add Distributions, StatsBase, StatsModels
-add RCall
-add PhyloNetworks
-add PhyloPlots # do this after adding PhyloNetworks, to install a compatible version
+using Pkg
+Pkg.add("PhyloNetworks")
+Pkg.add("CairoMakie")
+Pkg.add(url = "https://github.com/jeetsukumaran/PhyloMakie.jl")
 ```
+
 Installation may take a while, especially if internet is slow.
 
 After this is done, type delete or backspace to go back to julian mode
 (exit from package mode). The julia prompt will go back to `julia>`.
-
-
-We will make use of R within Julia, and of some R functions
-in specific R packages.
-Install the `ape` and `viridis` packages in R:
-```r
-R> install.packages("viridis")
-R> install.packages("ape")
-```
diff --git a/topic2-getstarted.qmd b/topic2-getstarted.qmd
index ccabe5e..a299c07 100644
--- a/topic2-getstarted.qmd
+++ b/topic2-getstarted.qmd
@@ -12,8 +12,8 @@ Load the packages we will use:
 using CSV               # read/write CSV and similar formats
 using DataFrames        # versatile tabular data format
 using PhyloNetworks     # includes many utilities
-using PhyloPlots        # for plotting networks: via R
-using RCall             # run R within Julia
+using CairoMakie        # static-image Makie backend
+using PhyloMakie        # for plotting networks
 using StatsBase, StatsModels # basic stat functions, e.g. to build regression formulas
 using Distributions     # to get probabilities and quantiles of common distributions
 ```
@@ -32,8 +32,7 @@ and it will need to be rooted correctly later.
 #| label: fig-0-netsnaq
 #| fig-cap: "Polemonium network topology from SNaQ: needs rooting, branch lengths in coalescent units"
 net_snaq = readnewick("data/polemonium_network_fromSNaQ.phy");
-R"par"(mar=[0,0,0,0], cex=0.7); # 0 margins, cex<1 for smaller 'character expansion'
-plot(net_snaq; showedgelength=true, xlim=[0,18]); # increased limit to see full taxon labels
+plot(net_snaq; showedgelength=true, xlim=[0,18]) # increased limit to see full taxon labels
 ```
 
 then the trait data
@@ -77,9 +76,3 @@ size(traits_indiv) # number of rows and number of columns
   a package with `add ...`, change the version of a package you already installed,
   check what packages and what version you're currently using with `status`, etc.
   Type backspace to return to julian mode.
-
-- R mode, after using the RCall package: type `$` to access R. This R session
-  has access to the variables created by Julia, and vice versa.
-  Type backspace to return to julian mode.
-  Doing `@rlibrary ggplot2` within julia provides access to the R package
-  ggplot2 package outside the R mode and with easy syntax.
diff --git a/topic4-netcalibration.qmd b/topic4-netcalibration.qmd
index 6855b97..3c7d410 100644
--- a/topic4-netcalibration.qmd
+++ b/topic4-netcalibration.qmd
@@ -9,8 +9,8 @@ If not done during the session before, load necessary packages
 using CSV               # read/write CSV and similar formats
 using DataFrames        # versatile tabular data format
 using PhyloNetworks     # includes many utilities
-using PhyloPlots        # for plotting networks: via R
-using RCall             # run R within Julia
+using CairoMakie        # static-image Makie backend
+using PhyloMakie        # for plotting networks
 using StatsBase, StatsModels
 ```
 
@@ -61,13 +61,13 @@ end
 # root the network correctly. Now we can use the short names
 rootatnode!(net_snaq, "micranthum") # 1 outgroup: micranthum. otherwise use rootonedge!
 # plot the network to see where we should rotate edges to uncross reticulations
-R"par"(mar=[0,0,0,0]); # change default margins to 0
-res = plot(net_snaq, shownodenumber=true);
-res[[:xmin, :xmax]] # (0.0, 12.1) : default x limits for this network
+res = plot(net_snaq, shownodenumber=true)
+display(res) # subfigure (a): each display() call becomes one fig-subcap panel
+Makie.data_limits(res.plot) # default x/y limits for this network
 for nodenumber in [-16, -17,-6,-4, -19,-21]
-  rotate!(net_snaq, nodenumber)
+  PhyloNetworks.rotate!(net_snaq, nodenumber) # qualified: Makie also exports rotate!
 end
-plot(net_snaq, xlim=[0,16]); # extend limits to show full taxon names
+plot(net_snaq, xlim=[0,16]) # subfigure (b): extend limits to show full taxon names
 ```
 
 ## input genetic distances
@@ -157,9 +157,8 @@ and peek at the resulting network:
 ```{julia}
 #| label: fig-1-netcal0
 #| fig-cap: "Polemonium network: after calibration, edges drawn proportional to their lengths"
-R"par"(mar=[0,0,0,0]);
-R"par"(cex=0.5) # decrease "character expansion" for smaller annotations later
-res = plot(net, useedgelength=true, showedgelength=true);
+res = plot(net, useedgelength=true, showedgelength=true)
+display(res)
 ```
 
 ## normalize the network height
@@ -189,9 +188,8 @@ for e in net.edge
     e.length /= rootage
 end
 getnodeages(net) |> maximum # 1.0, sanity check
-R"par"(mar=[0,0,0,0]);
-plot(net, useedgelength=true, xlim=[1,2.5], showgamma=true);
-plot(net, useedgelength=true, xlim=[1,2.5], style=:majortree, arrowlen=0.07);
+display(plot(net, useedgelength=true, xlim=[1,2.5], showgamma=true)) # subfigure (a)
+plot(net, useedgelength=true, xlim=[1,2.5], style=:majortree, arrowlen=0.07) # subfigure (b)
 ```
 
 Finally, let's save our calibrated network to a file:
diff --git a/topic5-phyloANOVA.qmd b/topic5-phyloANOVA.qmd
index 37ac694..b5f1762 100644
--- a/topic5-phyloANOVA.qmd
+++ b/topic5-phyloANOVA.qmd
@@ -6,7 +6,7 @@ format: html
 ```{julia}
 #| code-fold: true
 # code from prior sections
-using CSV, DataFrames, PhyloNetworks, PhyloPlots, RCall, StatsBase, StatsModels
+using CSV, DataFrames, PhyloNetworks, StatsBase, StatsModels
 ```
 
 Phylogenetic regression and phylogenetic ANOVA are for:
diff --git a/topic6-asr.qmd b/topic6-asr.qmd
index ca01c2a..6016399 100644
--- a/topic6-asr.qmd
+++ b/topic6-asr.qmd
@@ -6,7 +6,7 @@ format: html
 ```{julia}
 #| code-fold: true
 # code from prior sections
-using CSV, DataFrames, PhyloNetworks, PhyloPlots, RCall
+using CSV, DataFrames, PhyloNetworks, CairoMakie, PhyloMakie
 using StatsBase, StatsModels, PhyloTraits
 net = readnewick("data/polemonium_network_calibrated.phy");
 for tip in net.node tip.name = replace(tip.name, r"_2$" => s""); end
@@ -102,9 +102,8 @@ first(nodepred, 4)
 ```{julia}
 #| label: fig-3-asrmean
 #| fig-cap: "ancestral state reconstruction: species means conditional on data"
-R"par"(mar=[0,0,0,0]);
 plot(net, nodelabel=nodepred, nodecex=0.8, nodelabeladj=[1,-0.1],
-    tipoffset=0.1, xlim=[0,13]);
+    tipoffset=0.1, xlim=[0,13])
 ```
 
 ```{julia}
@@ -117,7 +116,6 @@ first(nodeint, 4)
 ```{julia}
 #| label: fig-3-asrint
 #| fig-cap: "ancestral state reconstruction: 95% prediction interval"
-R"par"(mar=[0,0,0,0]);
 plot(net, nodelabel=nodeint, nodecex=0.7, nodelabeladj=[1,-0.1],
-     tipoffset=0.1, xlim=[-0.1,13]);
+     tipoffset=0.1, xlim=[-0.1,13])
 ```
diff --git a/topic7-impactgeneflow.qmd b/topic7-impactgeneflow.qmd
index 598fbc1..9b566c4 100644
--- a/topic7-impactgeneflow.qmd
+++ b/topic7-impactgeneflow.qmd
@@ -6,7 +6,7 @@ format: html
 ```{julia}
 #| code-fold: true
 # code from prior sections
-using CSV, DataFrames, PhyloNetworks, PhyloPlots, RCall
+using CSV, DataFrames, PhyloNetworks, CairoMakie, PhyloMakie
 using StatsBase, StatsModels, PhyloTraits
 net = readnewick("data/polemonium_network_calibrated.phy");
 for tip in net.node tip.name = replace(tip.name, r"_2$" => s""); end
@@ -29,8 +29,7 @@ We can delete all the "minor" hybrid edges (with γ<0.5) as shown below.
 #| label: fig-4-majortree
 #| fig-cap: "major tree, drawn proportional to edge lengths"
 tree = majortree(net)
-R"par"(mar=[0,0,0,0]);
-plot(tree, tipoffset=0.05, useedgelength=true, xlim=[1,2.5]);
+plot(tree, tipoffset=0.05, useedgelength=true, xlim=[1,2.5])
 ```
 
 ```{julia}
@@ -107,7 +106,6 @@ the network and ask to see the edge numbers, as shown below.
 
 ```{julia}
 #| include: false
-R"par"(mar=[0,0,0,0]);
 plot(net, tipoffset=0.05, showedgenumber=true, xlim=[1,13]);
 ```
 
diff --git a/topic8-discrete.qmd b/topic8-discrete.qmd
index dce0265..f897596 100644
--- a/topic8-discrete.qmd
+++ b/topic8-discrete.qmd
@@ -7,7 +7,7 @@ format: html
 #| code-fold: true
 #| output: false
 # code from prior sections
-using CSV, DataFrames, PhyloNetworks, PhyloPlots, RCall
+using CSV, DataFrames, PhyloNetworks, CairoMakie, PhyloMakie
 using StatsBase, StatsModels, PhyloTraits
 net = readnewick("data/polemonium_network_calibrated.phy");
 for tip in net.node tip.name = replace(tip.name, r"_2$" => s""); end
@@ -74,10 +74,9 @@ that the node numbers match.
 #|   - "showing node numbers"
 #|   - "showing the posterior probability of state 'hi'"
 #| layout-ncol: 2
-R"par"(mar=[0,0,0,0]);
-plot(fit.net, shownodenumber=true, showgamma=true, tipoffset=0.1, xlim=[0,15]);
+display(plot(fit.net, shownodenumber=true, showgamma=true, tipoffset=0.1, xlim=[0,15])) # subfigure (a)
 plot(fit.net, nodelabel=select(asr, :nodenumber, :hi), nodelabeladj=[1,-0.1],
-     tipoffset=0.1, xlim=[0,15]);
+     tipoffset=0.1, xlim=[0,15]) # subfigure (b)
 ```
 
 ## effect of gene flow
diff --git a/topic9-visualization.qmd b/topic9-visualization.qmd
index b6998eb..8249e36 100644
--- a/topic9-visualization.qmd
+++ b/topic9-visualization.qmd
@@ -9,7 +9,7 @@ format:
 #| code-fold: true
 #| output: false
 # code from prior sections
-using CSV, DataFrames, PhyloNetworks, PhyloPlots, RCall
+using CSV, DataFrames, PhyloNetworks, CairoMakie, PhyloMakie
 using StatsBase, StatsModels, PhyloTraits
 net = readnewick("data/polemonium_network_calibrated.phy");
 for tip in net.node tip.name = replace(tip.name, r"_2$" => s""); end
@@ -27,6 +27,12 @@ For each example, we suggest that you go step by step and inspect each element
 in the code. The more the code makes sense, the more we can customize it later
 for our own needs on other data sets.
 
+Each example below renders the network with `plot!` into a plain Makie `Axis`,
+then composes native Makie primitives (`scatter!`, `text!`, `Makie.pie!`,
+`Legend`) on top of it. `node_positions`/`edge_positions` read node and edge
+coordinates directly off the rendered plot, so we never need to know a taxon's
+position in advance.
+
 ## discrete trait data at the tips
 
 Following the example of a [discrete](topic8-discrete.qmd) trait,
@@ -36,37 +42,46 @@ of high or low elevation, let's visualize the data at the tips.
 #| code-fold: true
 #| label: fig-6-tips-discrete
 #| fig-cap: "showing a discrete trait at the tips"
-R"par"(mar=[0,0,0,0]);
-# plot and save the "res"ult to get point coordinates, to use for adding annotation on top
-res = plot(net, tipoffset=0.5, xlim=[0.5,16]);
-res[[:xmin, :xmax, :ymin, :ymax]] # x and y limits
-res[:node_data]  # info to add node annotations
-res[:edge_data]  # info to add edge annotations
-
-# find order "o" in which species from data are listed in the network -- and in res
+figure = Figure(size = (900, 500))
+axis = Axis(figure[1, 1])
+hidedecorations!(axis)
+hidespines!(axis)
+plot_handle = plot!(axis, net; tipoffset=0.5, xlim=(0.5, 16))
+
+# query node/edge coordinates, to use for adding annotations on top
+node_table = node_positions(plot_handle)  # info to add node annotations
+edge_table = edge_positions(plot_handle)  # info to add edge annotations
+
+# find order "o" in which species from data are listed in the network -- and in node_table
 o = [findfirst(isequal(tax), dat.morph) for tax in tiplabels(net)]
 dat.morph[o] == tiplabels(net) # should be true, if order o is as intended
-tips = res[:node_data][!,:lea]
-dat.morph[o] == res[:node_data][tips,:name] # should be true
+tip_rows = filter(:isleaf => identity, node_table)
+dat.morph[o] == tip_rows.name # should be true
 
 # next: add grey & red points at the leaves
-tip_col = map(x -> (x=="lo" ? "grey" : "red"), dat.elevation[o])
-R"points"(
-    x=res[:node_data][tips,:x] .+0.1,
-    y=res[:node_data][tips,:y],
-    pch=16, col=tip_col, cex=1.5);
+tip_col = map(x -> (x=="lo" ? :grey : :red), dat.elevation[o])
+scatter!(axis, tip_rows.x .+ 0.1, tip_rows.y; color=tip_col, markersize=15)
 
 # next: add a legend to say which color is for which state
-R"legend"(x=1, y=19, legend=["hi","lo"], pch=16,
-    col=["red","grey"], title="elevation",
-    bty="n", var"title.adj"=0);
-    # var"" to allow for a dot in the variable name: R's fault...
+Legend(
+    figure[1, 2],
+    [MarkerElement(color=c, marker=:circle, markersize=15) for c in (:red, :grey)],
+    ["hi", "lo"];
+    title="elevation",
+)
 
 # next: add γ's for gene flow edges
-hybminor = res[:edge_data].min
-hybdf = res[:edge_data][hybminor, [:x,:y,:gam]]
-R"text"(hybdf.x .- 0.1, hybdf.y + 0.5.*[-1,1,1], hybdf.gam,
-        col="deepskyblue", cex=0.75);
+minor_hybrid_rows = filter(row -> row.ishybrid && !row.ismajor, edge_table)
+text!(
+    axis,
+    minor_hybrid_rows.x .- 0.1,
+    minor_hybrid_rows.y .+ 0.5 .* [-1, 1, 1];
+    text = string.(round.(minor_hybrid_rows.gamma; digits=2)),
+    color = :deepskyblue,
+    fontsize = 12,
+)
+
+figure
 ```
 
 ## ancestral probabilities
@@ -86,24 +101,41 @@ colnames = names(asr)[3:end] # to get the correct state - probability match
 asr[!,:fake] .= ""; # to add fake internal node labels later: and extract their positions
 asr # just to check
 
-coltrait = ["red","grey"] # or anything else: names that R knows how to interpret
+coltrait = (:red, :grey) # or anything else: a color Makie knows how to interpret
 
 # start the plot
-R"par"(mar=[0,0,0,0]);
-res = plot(fit.net, tipoffset=0.5, xlim=[0.5,16], arrowlen=0.15,
-           nodelabel = asr[:,[:nodenumber, :fake]]);
-ndf = res[:node_data] # had locations of internal nodes, this time
+figure = Figure(size = (900, 500))
+axis = Axis(figure[1, 1])
+hidedecorations!(axis)
+hidespines!(axis)
+plot_handle = plot!(
+    axis, fit.net;
+    tipoffset=0.5, xlim=(0.5, 16), arrowlen=0.15,
+    nodelabel = asr[:,[:nodenumber, :fake]],
+)
+node_table = node_positions(plot_handle) # had locations of internal nodes, this time
 
 # add pie charts, using locations of internal nodes
 for i in 1:nrow(asr) # loop over each row in the ancestral state reconstruction data frame
-  ii = findfirst(isequal(string(asr[!,:nodenumber][i])), ndf[!,:num]);
-  colpp = Vector(asr[i,colnames]);
-  R"ape::floating.pie.asp"(ndf[ii,:x], ndf[ii,:y], colpp,
-                           radius=0.2, col=coltrait);
+  ii = findfirst(isequal(asr[!,:nodenumber][i]), node_table.number)
+  colpp = Vector(asr[i,colnames])
+  Makie.pie!(
+      axis,
+      Makie.Point2f(node_table.x[ii], node_table.y[ii]),
+      colpp;
+      radius = 0.2,
+      color = collect(coltrait),
+  )
 end
 # add legend with correct mapping of color -> state
-R"legend"(x=1, y=19, legend=colnames, pch=21, var"pt.bg"=coltrait,
-          bty="n", title="elevation", var"title.adj"=0, var"pt.cex"=1.5);
+Legend(
+    figure[1, 2],
+    [PolyElement(color=c) for c in coltrait],
+    colnames;
+    title = "elevation",
+)
+
+figure
 ```
 
 ## continuous trait data at the tips
@@ -115,32 +147,55 @@ at the tips.
 #| code-fold: true
 #| label: fig-6-tips-continuous
 #| fig-cap: "bar plot to visualize continuous traits at the tips. red: above average. grey: below average"
-R"par"(mar=[2,0,1.5,0]);
 # plot the network with a large tip offset to leave space for bars
-res = plot(net, tipoffset=2.2, xlim=[0.5,17]);
+figure = Figure(size = (900, 550))
+axis = Axis(figure[1, 1])
+hidedecorations!(axis)
+hidespines!(axis)
+plot_handle = plot!(axis, net; tipoffset=2.2, xlim=(0.5, 17))
+tip_rows = filter(:isleaf => identity, node_positions(plot_handle))
 
 # create standardized version of elevation, such that 0 corresponds to the mean,
 # and such that the range covers an interval of length 2:
 # for the bars to fit between the tips and the taxon names
-o = [findfirst(isequal(tax), traits.morph) for tax in res[:node_data].name] # ordering
+o = [findfirst(isequal(tax), traits.morph) for tax in tip_rows.name] # ordering
 intervallength = 2
 std_elev = intervallength .* standardize(UnitRangeTransform, traits.elevation[o])
 std_elev .-= mean(std_elev) # now mean = 0, interval length still as desired
-linecol = [(el < 0 ? "grey" : "red") for el in std_elev] # grey if elevation < mean, red if elevation > mean
+linecol = [(el < 0 ? :grey : :red) for el in std_elev] # grey if elevation < mean, red if elevation > mean
 m = minimum(std_elev)    # new minimum elevation, after "standardization"
-x0 = res[:node_data][1,:x] + 0.1 # x where the smallest bar should extend
+x0 = tip_rows.x[1] + 0.1 # x where the smallest bar should extend
 xmean = x0 - m           # x where the mean value will go
-# create the bars
-R"segments"(x0 = xmean, x1 = xmean .+ std_elev,
-            y0=res[:node_data].y, col=linecol,
-            lwd=10, lend=1); # thick lines, line ends of "butt" type
-
-# label the horizontal axis to show the original min and max elevations
-min_evel, max_elev = round.(extrema(traits.elevation[o]), digits=2);
-R"axis"(at=[x0, x0+intervallength],
-        labels=round.([min_evel,max_elev], digits=2),
-        side=1, line=-0.5, tck=-0.01);
-R"text"(x=x0, y=21, "elevation (km)", adj=0);
+# create the bars: linesegments! takes one flat vector of alternating
+# (start, end) points, with one color per point
+bar_points = Makie.Point2f[]
+bar_colors = Symbol[]
+for (elev, y, col) in zip(std_elev, tip_rows.y, linecol)
+    push!(bar_points, Makie.Point2f(xmean, y))
+    push!(bar_points, Makie.Point2f(xmean + elev, y))
+    push!(bar_colors, col, col)
+end
+linesegments!(axis, bar_points; color = bar_colors, linewidth = 10)
+
+# add a small reference scale to show the original min and max elevations.
+# label positions are in data units (not a pixel offset), so Makie's
+# automatic axis limits expand to include them rather than clipping them.
+min_elev, max_elev = round.(extrema(traits.elevation[o]), digits=2)
+scale_y = minimum(tip_rows.y) - 1.5
+lines!(axis, [x0, x0 + intervallength], [scale_y, scale_y]; color = :black)
+text!(
+    axis,
+    [x0, x0 + intervallength], fill(scale_y - 0.8, 2);
+    text = string.([min_elev, max_elev]),
+    align = (:center, :top),
+)
+text!(
+    axis, x0 + intervallength / 2, scale_y - 1.8;
+    text = "elevation (km)",
+    align = (:center, :top),
+)
+
+figure
 ```
 
 
@@ -164,31 +219,37 @@ fit_larea = phylolm(@formula(larea ~ 1), traits, net, tipnames=:morph,
 asr_larea = predict(ancestralreconstruction(fit_larea))
 asr_larea[!,:fake] .= ""; # fake empty labels
 
-
-# convert numerical ancestral states to colors, using a palette
-asr_larea_01 = standardize(UnitRangeTransform, asr_larea.prediction) # values in 0-1
-@rlibrary viridis
-mypalette = rcopy(viridis(256)) # 256 possible colors in the palette
-import CategoricalArrays: cut
-breaks = [i/256 for i in 0:256]
-asr_larea_index = convert(Vector{Int}, cut(asr_larea_01, breaks; extend=true, labels=1:256))
-asr_larea_colr = mypalette[asr_larea_index]
-
 # start the plot
-R"par"(mar=[0,0,0,0]);
-res = plot(net, tipoffset=0.5, xlim=[0.5,16],
-           nodelabel = asr_larea[:,[:nodenumber, :fake]]);
-
-# find order to match tips between asr_larea and res[:node_data]
-ndf = res[:node_data]
-o = [findfirst(isequal(nn), asr_larea.nodenumber) for nn in parse.(Int, ndf.num)]
-asr_larea.nodenumber[o] == parse.(Int, ndf.num) # should be true
-
-# add the colored circles
-R"points"(x=ndf.x, y=ndf.y, pch=16, col=asr_larea_colr[o], cex=1.5);
-
-# add legend
-m,M = string.(round.(extrema(asr_larea.prediction), digits=2))
-R"legend"(x=0, y=19, bty="n", adj=0, var"y.intersp"=0.5, border="NA",
-    legend = [m,"","","",M], fill = mypalette[[1, 64, 128, 192, 256]]);
+figure = Figure(size = (950, 500))
+axis = Axis(figure[1, 1])
+hidedecorations!(axis)
+hidespines!(axis)
+plot_handle = plot!(
+    axis, net;
+    tipoffset=0.5, xlim=(0.5, 16),
+    nodelabel = asr_larea[:,[:nodenumber, :fake]],
+)
+node_table = node_positions(plot_handle)
+
+# find order to match tips between asr_larea and node_table
+o = [findfirst(isequal(nn), asr_larea.nodenumber) for nn in node_table.number]
+asr_larea.nodenumber[o] == node_table.number # should be true
+
+# add the ancestral-state predictions as a continuous color gradient: no
+# manual palette, binning, or R round-trip needed, Makie interpolates directly
+scatter!(
+    axis, node_table.x, node_table.y;
+    color = asr_larea.prediction[o],
+    colormap = :viridis,
+    colorrange = extrema(asr_larea.prediction),
+    markersize = 15,
+)
+Colorbar(
+    figure[1, 2];
+    colormap = :viridis,
+    limits = extrema(asr_larea.prediction),
+    label = "log-leaflet area",
+)
+
+figure
 ```