Merge pull request #1 from laduplessis/master

Update to BEAST 2.7
genomescale · Aug 15, 2023 · 21af154 · 21af154
2 parents d88d4c5 + 1997d18
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diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
 ---
 author: Huw A. Ogilvie
 level: Intermediate
-title: StarBEAST2 v14 tutorial
+title: StarBEAST2 v1.0.0 tutorial
 subtitle: Estimating species trees using StarBEAST2
-beastversion: 2.5.0
+beastversion: 2.7.x
 ---
 
 
@@ -20,4 +20,6 @@ tree analyses using StarBEAST2. The first is basic species tree reconstruction u
 a strict nuclear clock rate.  The second is a relaxed clock analysis where a separate
 molecular clock rate is estimated for each species branch. The third is a
 _total evidence_ analysis where the times and rates and jointly estimated by integrating
-fossil data into the model.
+fossil data into the model.
+
+This tutorial is identical to the tutorial hosted [here](https://github.com/genomescale/starbeast2/releases/tag/v1.0.0).
diff --git a/data/tip_dates_canis.dat b/data/tip_dates_canis.dat
@@ -0,0 +1,24 @@
+Canis_adustus	0.000000
+Canis_anthus	0.000000
+Canis_antonii	1.200000
+Canis_armbrusteri	0.300000
+Canis_arnensis	1.500000
+Canis_chihliensis	1.200000
+Canis_dirus	0.012000
+Canis_edwardii	0.300000
+Canis_etruscus	1.700000
+Canis_falconeri	1.500000
+Canis_ferox	3.500000
+Canis_latrans	0.000000
+Canis_lepophagus	1.800000
+Canis_lupus	0.000000
+Canis_mesomelas	0.000000
+Canis_mosbachensis	0.500000
+Canis_palmidens	1.500000
+Canis_simensis	0.000000
+Canis_thooides	1.800000
+Canis_variabilis	0.500000
+Cuon_alpinus	0.000000
+Eucyon_davisi	4.900000
+Lycaon_pictus	0.000000
+Xenocyon_texanus	0.240000
diff --git a/figures/addMorphology.png b/figures/addMorphology.png
diff --git a/figures/birthDeathModel.png b/figures/birthDeathModel.png
diff --git a/figures/chainLength.png b/figures/chainLength.png
diff --git a/figures/changeTreePrior.png b/figures/changeTreePrior.png
diff --git a/figures/clockPriors.png b/figures/clockPriors.png
diff --git a/figures/clockRateHistogram.png b/figures/clockRateHistogram.png
diff --git a/figures/clockRateTrace.png b/figures/clockRateTrace.png
diff --git a/figures/cloneSiteModel.png b/figures/cloneSiteModel.png
diff --git a/figures/constantPopulations.png b/figures/constantPopulations.png
diff --git a/figures/densitree.png b/figures/densitree.png
diff --git a/figures/estimateMorphClock.png b/figures/estimateMorphClock.png
diff --git a/figures/fastaFileImport.png b/figures/fastaFileImport.png
diff --git a/figures/guessTaxonMap.png b/figures/guessTaxonMap.png
diff --git a/figures/hky.png b/figures/hky.png
diff --git a/figures/icytree.png b/figures/icytree.png
diff --git a/figures/installStarBEAST2.png b/figures/installStarBEAST2.png
diff --git a/figures/linkModels.png b/figures/linkModels.png
diff --git a/figures/managePackages.png b/figures/managePackages.png
diff --git a/figures/morphologyPartitions.png b/figures/morphologyPartitions.png
diff --git a/figures/sampledAncestorsDensitree.png b/figures/sampledAncestorsDensitree.png
diff --git a/figures/sampledAncestorsIcyTree.png b/figures/sampledAncestorsIcyTree.png
diff --git a/figures/samplingRate.png b/figures/samplingRate.png
diff --git a/figures/speciesTreeUCLN.png b/figures/speciesTreeUCLN.png
diff --git a/figures/strictClockModel.png b/figures/strictClockModel.png
diff --git a/figures/strictClockTemplate.png b/figures/strictClockTemplate.png
diff --git a/figures/taxonMap.png b/figures/taxonMap.png
diff --git a/figures/tipDates.png b/figures/tipDates.png
diff --git a/figures/tracerPosterior.png b/figures/tracerPosterior.png
diff --git a/figures/tracerUCLN.png b/figures/tracerUCLN.png
diff --git a/figures/treeAnnotator.png b/figures/treeAnnotator.png
diff --git a/figures/treeAnnotatorMeanHeights.png b/figures/treeAnnotatorMeanHeights.png
diff --git a/figures/uclnClockRates.png b/figures/uclnClockRates.png
diff --git a/main.tex b/main.tex
diff --git a/precooked_runs/CanisFBD/species.trees b/precooked_runs/CanisFBD/species.trees
diff --git a/precooked_runs/CanisFBD/starbeast.log b/precooked_runs/CanisFBD/starbeast.log
diff --git a/precooked_runs/CanisFBD/summary.tree b/precooked_runs/CanisFBD/summary.tree
diff --git a/precooked_runs/CanisPhylogeny/species.trees b/precooked_runs/CanisPhylogeny/species.trees
diff --git a/precooked_runs/CanisPhylogeny/starbeast.log b/precooked_runs/CanisPhylogeny/starbeast.log
diff --git a/precooked_runs/CanisPhylogeny/summary.tree b/precooked_runs/CanisPhylogeny/summary.tree
@@ -0,0 +1,28 @@
+#NEXUS
+
+Begin taxa;
+	Dimensions ntax=8;
+		Taxlabels
+			1 Canis_adustus
+			2 Canis_anthus
+			3 Canis_latrans
+			4 Canis_lupus
+			5 Canis_mesomelas
+			6 Canis_simensis
+			7 Cuon_alpinus
+			8 Lycaon_pictus
+			;
+End;
+Begin trees;
+	Translate
+		     1 Canis_adustus,
+		     2 Canis_anthus,
+		     3 Canis_latrans,
+		     4 Canis_lupus,
+		     5 Canis_mesomelas,
+		     6 Canis_simensis,
+		     7 Cuon_alpinus,
+		     8 Lycaon_pictus
+;
+tree TREE1 = ((1[&dmv={0.2088073165948103},dmv1=0.23939122526505865,dmv1_95%_HPD={0.09405655475206028,0.43202648308585406},dmv1_median=0.22338327646355996,dmv1_range={0.05472933811323015,0.8750873358563325},height=4.9675580965730517E-17,height_95%_HPD={0.0,4.440892098500626E-16},height_median=0.0,height_range={0.0,8.881784197001252E-16},length=1.9458219836591086,length_95%_HPD={1.1962436268997665,2.671704707200511},length_median=1.9514787594971705,length_range={0.5298965342919832,3.467945637658873}]:1.976520163325066,5[&dmv={0.4755491439308237},dmv1=0.49317525109284044,dmv1_95%_HPD={0.22046965127283302,0.8387253709721953},dmv1_median=0.4664621999062872,dmv1_range={0.13664909529146202,1.848496956345594},height=4.9675580965730517E-17,height_95%_HPD={0.0,4.440892098500626E-16},height_median=0.0,height_range={0.0,8.881784197001252E-16},length=1.9582517368753904,length_95%_HPD={1.2096765815312498,2.730391036310042},length_median=1.960116594885115,length_range={0.5298965342919832,3.495621635965402}]:1.976520163325066)[&CAheight_95%_HPD={1.2096765815312498,2.760048835889937},CAheight_mean=1.976520163325066,CAheight_median=1.9777120686885128,CAheight_range={0.5298965342919832,3.495621635965402},dmv={1.1313907840375572},dmv1=0.5248452279002448,dmv1_95%_HPD={0.04356507157609246,1.1774656277437419},dmv1_median=0.4534986028999813,dmv1_range={0.02757971709247715,2.592845948769848},height=1.8979366529498205,height_95%_HPD={1.1667499100241423,2.5777227880100027},height_median=1.9108441256981163,height_range={0.5298965342919832,3.0621639777263034},length=0.45349085248790266,length_95%_HPD={0.001238359241637621,1.067439074602934},length_median=0.3865581543079375,length_range={9.528245205023822E-4,2.0991661527974403},posterior=0.8186363005138175]:0.437973073059027,((((2[&dmv={0.09180598843304794},dmv1=0.21806393630653087,dmv1_95%_HPD={0.060835937185948215,0.42778135656063165},dmv1_median=0.19459304609348715,dmv1_range={0.033060728364793526,1.0734558682717203},height=4.8102983430502545E-17,height_95%_HPD={0.0,4.440892098500626E-16},height_median=0.0,height_range={0.0,4.440892098500626E-16},length=0.44772074490087677,length_95%_HPD={0.15436593717479807,0.7372842639542774},length_median=0.4353761820483628,length_range={0.034541730864977804,1.1134271408745025}]:0.49976887187490804,(3[&dmv={0.0767470584547076},dmv1=0.253188635935835,dmv1_95%_HPD={0.06429658096069868,0.5137726289076897},dmv1_median=0.22308294178297625,dmv1_range={0.031920394302140435,1.6855624458955913},height=4.628370392896431E-17,height_95%_HPD={0.0,4.440892098500626E-16},height_median=0.0,height_range={0.0,8.881784197001252E-16},length=0.4001668251303822,length_95%_HPD={0.1416333476538698,0.66857304932108},length_median=0.3912010315237364,length_range={0.05114783039118853,1.0394841850099872}]:0.40833807010752154,4[&dmv={0.09364185803353339},dmv1=0.2605784376162141,dmv1_95%_HPD={0.04799611481850444,0.5611989066050884},dmv1_median=0.21910677452675437,dmv1_range={0.032291737878953564,2.721396477994346},height=4.7332102285782954E-17,height_95%_HPD={0.0,4.440892098500626E-16},height_median=0.0,height_range={0.0,8.881784197001252E-16},length=0.364497177791491,length_95%_HPD={0.13435551450706207,0.6073442567893697},length_median=0.3554235559597205,length_range={0.034541730864977804,0.8725740979171586}]:0.40833807010752154)[&CAheight_95%_HPD={0.1427693277459885,0.6704524803361576},CAheight_mean=0.4083380701075216,CAheight_median=0.3994374354097252,CAheight_range={0.05114783039118853,1.0394841850099872},dmv={0.23252085291680497},dmv1=0.4733436288014526,dmv1_95%_HPD={0.0587309657023206,1.0182561506552696},dmv1_median=0.4189565065837083,dmv1_range={0.03358181299352933,2.329149242189787},height=0.3533222716991124,height_95%_HPD={0.11410176101375114,0.565401442686686},height_median=0.3476416842506517,height_range={0.05114783039118853,0.8725740979171586},length=0.1675426851369384,length_95%_HPD={1.4047190362509454E-4,0.40686230058582185},length_median=0.14216183615312483,length_range={1.4047190362509454E-4,0.7838278676259574},posterior=0.5454797944729899]:0.0914308017673865)[&CAheight_95%_HPD={0.24899092976247705,0.7777991240585036},CAheight_mean=0.4997688718749081,CAheight_median=0.48984806634272315,CAheight_range={0.13097022189050245,1.1134271408745025},dmv={0.9963378754101173},dmv1=0.5606780631214876,dmv1_95%_HPD={0.19244029591951878,1.0199183546587869},dmv1_median=0.5279821677467459,dmv1_range={0.10027565792700968,2.1160737788396253},height=0.4993351254328313,height_95%_HPD={0.24899092976247705,0.7764965950132758},height_median=0.4893380642608314,height_range={0.13097022189050245,1.1134271408745025},length=0.6137809208007804,length_95%_HPD={0.12794666505008778,1.0698728420759833},length_median=0.6079273010861441,length_range={0.033611239692632466,1.5768327782793112},posterior=0.9977780863768921]:0.6205466649694258,6[&dmv={0.12051336567441157},dmv1=0.10364512511042971,dmv1_95%_HPD={0.01925602917141031,0.21545992614251824},dmv1_median=0.09235534488631066,dmv1_range={0.00945992575792777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+End;