https://github.com/4ment/sts-test
Science Score: 33.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
1 of 9 committers (11.1%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary
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Repository
Basic Info
- Host: GitHub
- Owner: 4ment
- License: gpl-3.0
- Language: C++
- Default Branch: master
- Size: 8.86 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
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, andphylmodules. Note that debian & ubuntu up to 16.04 include v2.1.0 which is too old. Bio++ should be installed from source using thebpp-setup.shscript on these systems. - cmake
- gsl version 1.16 Note that gsl v2 is not currently supported.
- nlopt
- beagle version 2.1 (Optional)
- google test this is libgtest on debian/ubuntu (Optional)
Compiling
- Install dependencies
- 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.
Owner
- Name: Mathieu Fourment
- Login: 4ment
- Kind: user
- Location: Australia
- Company: University of Technology Sydney
- Repositories: 58
- Profile: https://github.com/4ment
GitHub Events
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Committers
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Top Committers
| Name | Commits | |
|---|---|---|
| Connor McCoy | c****y@f****g | 371 |
| Erick Matsen | m****n@f****g | 71 |
| Brian Claywell | b****l@f****g | 59 |
| Mathieu Fourment | m****t@g****m | 50 |
| Aaron Darling | a****g@u****u | 49 |
| Aaron Gallagher | h****t@g****m | 27 |
| Chris Warth | c****h@f****g | 2 |
| Dan Fornika | d****a@g****m | 1 |
| Erick Matsen | m****n@f****g | 1 |
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