diff --git a/README.md b/README.md index 2480902..683deae 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,27 @@ BEAST 2 implementation of a stochastic dollo model where sequence elements are a +## Installation instructions + + +This package requires BEAST 2.7 or newer + +1. Launch BEAUti +2. Click on File -> Manage Packages +3. Install IndelDollo. If IndelDollo is not in the list of packages, you may need to add an extra package repository as follows: + +- click the packager repositories button. A dialog pops up. +- click the Add URL button. A dialog is shown where you can enter https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra-2.7.xml +- click the OK button. There should be an extra entry in the list. +- click Done +- After a short delay, IndelDollo should appear in the list of packages. + + + +## Running IndelDollo + + +Please see the examples/ folder for working XML files. At this stage, IndelDollo analyses cannot be generated using BEAUti diff --git a/examples/AARS_class1.xml b/examples/AARS_class1.xml new file mode 100644 index 0000000..5907196 --- /dev/null +++ b/examples/AARS_class1.xml @@ -0,0 +1,682 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + beast.base.inference.distribution.Uniform + + beast.base.inference.distribution.Exponential + + beast.base.inference.distribution.LogNormalDistributionModel + + beast.base.inference.distribution.Normal + + beast.base.inference.distribution.Beta + + beast.base.inference.distribution.Gamma + + beast.base.inference.distribution.LaplaceDistribution + + beast.base.inference.distribution.Prior + + beast.base.inference.distribution.InverseGamma + + beast.base.inference.distribution.OneOnX + + + + + + + + + + + + + 1.0 + 0.1 + 1.0 + + + 1.0 + + + + + 1.0 + + + + + 14 + 1.0 + 0.1 + 0 + 0 + false + 0.05 + + + + + + + + + + + + 1.0 + + + + + + + + + + 0.01 + 1.0 + 0.01 + 1.0 + 0.1 + + + + + + + + + + + + + 1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 174 67 59 440 72 885 84 76 194 106 132 205 204 67 67 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/examples/AARS_class2.xml b/examples/AARS_class2.xml new file mode 100644 index 0000000..48ff66a --- /dev/null +++ b/examples/AARS_class2.xml @@ -0,0 +1,682 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + beast.base.inference.distribution.Uniform + + beast.base.inference.distribution.Exponential + + beast.base.inference.distribution.LogNormalDistributionModel + + beast.base.inference.distribution.Normal + + beast.base.inference.distribution.Beta + + beast.base.inference.distribution.Gamma + + beast.base.inference.distribution.LaplaceDistribution + + beast.base.inference.distribution.Prior + + beast.base.inference.distribution.InverseGamma + + beast.base.inference.distribution.OneOnX + + + + + + + + + + + + + 1.0 + 0.1 + 1.0 + + + 1.0 + + + + + 1.0 + + + + + 14 + 1.0 + 0.1 + 0 + 0 + false + 0.05 + + + + + + + + + + + + 1.0 + + + + + + + + + + 0.01 + 1.0 + 0.01 + 1.0 + 0.1 + + + + + + + + + + + + + 1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 83 44 67 55 100 174 53 27 180 43 38 191 99 140 69 77 36 68 46 53 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +