Merge branch 'main' of https://github.com/jordandouglas/MutationTree into main

Author: jordandouglas

README.md

@@ -1,7 +1,7 @@
 # BeastMap
-A BEAST 2 package for counting the number of synonymous, non-synonymous, and indel mutations on each branch
-
+A BEAST 2 package for counting the number of synonymous, non-synonymous, and indel mutations on each branch. The method first performs ancestral sequence reconstruction on the internal nodes, and then uses stochastic mapping to sample a mutation pathway along each branch. This all happens during MCMC, and the package is compatible with a wide range of existing BEAST 2 site, clock, and tree models.
 
+Warning: package is currently in pre-pre-release. It has passed the simulation studies, but the code is still quite volatile.
 
 ## Install
 
@@ -21,6 +21,9 @@ unzip -o tmp.zip
 ```
 
 
+Or you can download the zip file directly from the releases section. Please make sure to install the `CodonSubstModels` package too, as that is a dependency.
+
+
 ## Available counters
 
 Each counter requires a ```BranchMutationSampler```, which will stochastically sample the mutations at the time of logging. This ensures that the various mutation summarisers below will be in harmony.
@@ -31,12 +34,12 @@ Counts the total number of substitutions per branch.
 ```<sampler spec="beastmap.logger.mut.SubstitutionSum" sampler="@mutationsampler" />```
 
 ### SynonymousSubstSum
-Counts the total number of synonymous substitutions per branch. Requirements: **nucleotide** data. Options: code (default: universal); readingFrame (default: 1).
+Counts the total number of synonymous substitutions per branch. Requirements: **nucleotide** or **codon** data. Options: code (default: universal); readingFrame (default: 1).
 
 ```<sampler spec="beastmap.logger.mut.SynonymousSubstSum" sampler="@mutationsampler" code="universal" readingFrame="1"/>```
 
 ### NonSynonymousSubstSum
-Counts the total number of non-synonymous substitutions per branch. Requirements: **nucleotide** data. Options: code (default: universal); readingFrame (default: 1).
+Counts the total number of non-synonymous substitutions per branch. Requirements: **nucleotide** or **codon** data. Options: code (default: universal); readingFrame (default: 1).
 
 ```<sampler spec="beastmap.logger.mut.NonSynonymousSubstSum" sampler="@mutationsampler"  code="universal" readingFrame="1"/>```
 
@@ -56,7 +59,23 @@ Counts the total number of substitutions per branch (purine to pyrimidine or vic
 ``` <sampler spec="beastmap.logger.mut.NucleotideTransitionCounter" sampler="@mutationsampler" />```
 
 
+### AminoAcidClassChanges
+Counts the total number of amino acid substitutions per branch such that the amino acid chnages to a different functional class. Requirements: **amino acid** data. These classes are based on the BLOSUM62 matrix non-polar: {IVLM}, amide/amine: {DENQ}, basic: {HKR}, aromatic: {FWY}, small/polar: {AST}, cysteine: {C}, glycine: {G}, proline: {P}.
+
+``` <sampler spec="beastmap.logger.mut.AminoAcidClassChanges" sampler="@mutationsampler" />```
+
+
+### AminoAcidClassRemains
+Counts the total number of amino acid substitutions per branch such that the amino acid remains in the same functional class. Requirements: **amino acid** data.
 
+``` <sampler spec="beastmap.logger.mut.AminoAcidClassRemains" sampler="@mutationsampler" />```
+
+
+### SubstitutionSummer
+
+Takes one of the other per-branch counters and adds all the numbers together across the whole tree
+
+``` <log spec="beastmap.logger.SubstitutionSummer" counter="@ID_OF_COUNTER"  />```
 
 
 ## Setting up counters in XML
@@ -70,11 +89,16 @@ Append the following loggers to the bottom of the XML file to count the number o
           <sampler id="SubstitutionSum" spec="beastmap.logger.mut.SubstitutionSum" sampler="@mutationsampler" />
           <sampler id="SynonymousSubstSum" spec="beastmap.logger.mut.SynonymousSubstSum" sampler="@mutationsampler" code="universal" readingFrame="1"/>
           <sampler id="NonSynonymousSubstSum" spec="beastmap.logger.mut.NonSynonymousSubstSum" sampler="@mutationsampler"  code="universal" readingFrame="1"/>
-          <sampler id="FromToSubstSum" spec="beastmap.logger.mut.FromToSubstSum" sampler="@mutationsampler" from="A" to="A" />
+          <sampler id="FromToSubstSum" spec="beastmap.logger.mut.FromToSubstSum" sampler="@mutationsampler" from="A" to="G" />
           <sampler id="NucleotideTransitionCounter" spec="beastmap.logger.mut.NucleotideTransitionCounter" sampler="@mutationsampler" />
+          <sampler id="NucleotideTransversionCounter" spec="beastmap.logger.mut.NucleotideTransversionCounter" sampler="@mutationsampler" />
+          <sampler id="SubstitutionSumFiltered" spec="beastmap.logger.mut.SubstitutionSum" sampler="@mutationsampler" filter="2,1-99\3" />
+
+          <!-- This will log the ancestral sequences onto the tree -- it will make the tree files quite large so turn it off if you dont want it -->
+          <sampler id="AncestralSequenceLogger" spec="beastmap.logger.AncestralSequenceLogger" sampler="@mutationsampler"/>
 
           <sampler id="NucleotideTransversionCounter" spec="beastmap.logger.mut.NucleotideTransversionCounter">
-            <sampler id="mutationsampler" spec="beastmap.evolution.BranchMutationSampler" tag="seq" useAmbiguities="true" >
+            <sampler id="mutationsampler" spec="beastmap.evolution.BranchMutationSampler" tag="seq" useAmbiguities="true" substModelIsNodeDependent="false" burnin="50000" >
                <tree idref="tree" />
                <siteModel idref="siteModelID" />
                <branchRateModel idref="clockModelID" />
@@ -97,4 +121,4 @@ You can also place these loggers in the trace file as well as the tree file to e
 
 ## Examples
 
-See the beastmap.xml file in examples.
+See the xml file in examples.