Sequential Tree Sampler for online phylogenetics
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README.md

Sequential Tree Sampler (STS)

The sequential tree sampler implements a prototype of online phylogenetics, updating a posterior distribution generated by MrBayes with new sequences. The algorithm has been described and its performance evaluated in a manuscript. The scripts used to generate the figures can be found here.

Dependencies

  • smctc - included as git submodule (git submodule update --init)
  • lcfit - included as git submodule (git submodule update --init)
  • Bio++ version 2.2.0 core, seq, and phyl modules. Note that debian & ubuntu up to 16.04 include v2.1.0 which is too old. Bio++ should be installed from source using the bpp-setup.sh script on these systems. Alternatively, the source code of version 2.3.0 for each module can be dowloaded from github in the releases section
  • cmake
  • gsl version 1.16 Note that gsl v2 is not currently supported.
  • nlopt
  • boost boost
  • beagle version 2.1 (Optional)
  • google test this is libgtest on debian/ubuntu (Optional)

Compiling

  1. Install dependencies
  2. run make

Binaries will be build in _build/release

Adding taxa to an existing posterior

The tool sts-online adds taxa to an existing posterior tree sample. sts-online operates on a fasta file and tree file in nexus format. The fasta file must contain an alignment with a superset of the taxa in the tree file.

Currently only the Jukes-Cantor model is supported.

Example invocation

sts-online -b 250 -p 2 --proposal-method lcfit 10taxon-01.fasta 10tax_trim_t1.t 10tax_trim_t1.sts.json

In this example, we use an alignment containing 10 sequences and a posterior sample of trees generated by MrBayes with an alignment that does not contain the sequence labeled t1. sts-online ignores the first 250 trees from 50tax_trim.run1.t and uses a particle factor of 2. The 10tax_trim_t1.sts.json file will contain the updated trees.