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| Original file line number | Diff line number | Diff line change |
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| physher | ||
| ======= | ||
| # physher | ||
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| [](https://github.com/4ment/physher/actions/workflows/cmake.yml) | ||
| [](https://www.gnu.org/licenses/gpl-2.0) | ||
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| ## About physher | ||
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| ``physher`` is a program for estimating evolutionary rates and divergence times from genetic, amino acid, codon, and generic data. | ||
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| The current version of physher is incompatible with the first version. | ||
| Documentation for installing physher1 can be found [here](https://github.com/4ment/physher/wiki/Install) and the manual is located [here](https://github.com/4ment/physher/wiki/Usage). | ||
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| Introduction | ||
| ------------ | ||
| ## Getting Started | ||
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| Physher is a maximum likelihood-based method for estimating evolutionary rates and divergence times from genetic, amino acid, codon, and generic data. Phylogenetic trees should be open with Figtree from this [website](http://tree.bio.ed.ac.uk/software/figtree/) or [Seqotron](https://github.com/4ment/seqotron/). | ||
| A C compiler such as ``gcc`` or ``clang`` is required. It is also requires the [GSL] library. | ||
| On Debian-based systems, dependencies can be installed via ``apt``: | ||
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| For more details about the configuration file and command line arguments see the [wiki](https://github.com/4ment/physher/wiki/Usage) | ||
| ```bash | ||
| sudo apt install gcc gsl | ||
| ``` | ||
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| On MacOS, dependencies can be installed using a package manager such as [Homebrew](https://brew.sh). | ||
| ```bash | ||
| brew install llvm gsl | ||
| ``` | ||
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| Features | ||
| -------- | ||
| Other package managers such as [conda](https://conda.io) and [MacPorts](https://www.macports.org) can also be used to install dependencies. | ||
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| * Substitution models: | ||
| * Nucleotide: Reversible: GTR, HKY, K80, and JC69 + any models using encoding 00000 ... 01234. Non reversible: UREV (stationary) and NONSTAT (non stationary). | ||
| * Codon: GY94. | ||
| * Amino acid: Dayhoff, LG, and WAG. | ||
| * General: custom state space (e.g. phylogeography). | ||
| ### Dependencies | ||
| - [GSL] | ||
| - [sse2neon] (already included in physher) | ||
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| * Rate heterogeneity among sites: | ||
| * Gamma distributed. | ||
| * Proportion of invariant site. | ||
| ### Installation | ||
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| To build ``physher`` from source you can run | ||
| ```bash | ||
| git clone https://github.com/4ment/physher | ||
| cmake -S physher/ -B physher/build | ||
| cmake --build physher/build/ --target install | ||
| ``` | ||
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| ### Check install | ||
| If the installation was successful, this command should print the version of `physher` | ||
| ```bash | ||
| physher | ||
| ``` | ||
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| * Molecular clock: | ||
| * No clock | ||
| * Strict clock: constant rate across lineages. | ||
| * Local clock: monophyletic lineages evolve at the same rate. | ||
| * Discrete clock: a discrete distribution of rates is assigned to lineages without any restriction on the rate distribution. | ||
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| * Search algorithms for clock models: | ||
| * Greedy algorithm (local clock only). | ||
| * Genetic algorithm (discrete clock only). | ||
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| * Topology search: | ||
| * Nearest neighbor interchange (NNI) | ||
| ### Building C++ wrappers (optional) | ||
| A subset of physher's functionalities is exposed in C++ wrappers. These wrappers are used in [torchtree](https://github.com/4ment/torchtree), a python program, through bindings and [torchtree-physher](https://github.com/4ment/torchtree-physher). | ||
| A C++ compiler such as g++ or clang++ is required. Compilers can be installed using ``apt`` or ``homebrew`` | ||
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| * Confidence intervals | ||
| * Non-parametric bootstrap (Normal and percentile) using _bootstrap_ program (only available for strict clock models). | ||
| ```bash | ||
| git clone https://github.com/4ment/physher | ||
| cmake -S physher/ -B physher/build -DBUILD_CPP_WRAPPER=on | ||
| cmake --build physher/build/ --target install | ||
| ``` | ||
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| * Model averaging of divergence times and substitution rate | ||
| * Using modelavg program (only available using the genetic algorithm with discrete clocks). | ||
| ### Testing (optional) | ||
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| ```bash | ||
| cmake -S physher/ -B physher/build -DBUILD_TESTING=on | ||
| cmake --build physher/build/ --target install | ||
| ctest --test-dir physher/build/ | ||
| ``` | ||
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| Getting started | ||
| --------------- | ||
| ## Quick start | ||
| ```bash | ||
| cd examples/fluA | ||
| physher JC69-time-ELBO.json | ||
| ``` | ||
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| [Install physher](https://github.com/4ment/physher/wiki/Install) | ||
| ## physher in action | ||
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| [Online manual](https://github.com/4ment/physher/wiki/Usage) | ||
| Some examples of projects using ``physher`` | ||
| - [marginal-experiments](https://github.com/4ment/marginal-experiments): Evaluation of 19 dubious ways to compute marginal likelihood estimates. [10.1093/sysbio/syz046](https://doi.org/10.1093/sysbio/syz046). | ||
| - [phylostan](https://github.com/4ment/phylostan/tree/master/examples): Comparison of phylostan and ``physher`` using variational inference. [10.1101/702944](https://doi.org/10.1101/702944). | ||
| - [gradient-benchmark](https://github.com/4ment/gradient-benchmark): Benchmarking of automatic differentiation and analical gradients. [10.1093/gbe/evad099](https://doi.org/10.1093/gbe/evad099) | ||
| - [torchtree-physher](https://github.com/4ment/torchtree-physher): Plugin provinding fast calculation of phylogenetic functions in ``physher`` to [torchtree]. | ||
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| ## License | ||
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| Associated programs | ||
| ------------------------- | ||
| Distributed under the GPLv2 License. See [LICENSE](LICENSE) for more information. | ||
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| * _bootstrap_: calculate confidence intervals using bootstrap trees generated by a strict clock with _physher_. Every tree need to have the same topology. | ||
| * _simultron_: simulate nucleotide data given a fixed tree topology. | ||
| * _modelavg_: model average of trees generated by genetic algorithm with a discrete clock. | ||
| ## Citing physher | ||
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| Fourment M and Holmes EC. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. _BMC Evolutionary Biology_, 2014. doi: [10.1186/s12862-014-0163-6](https://doi.org/10.1186/s12862-014-0163-6) | ||
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| Reference | ||
| --------- | ||
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| Fourment M and Holmes EC. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology 14:163, 2014. | ||
| [GSL]: https://www.gnu.org/software/gsl | ||
| [sse2neon]: https://github.com/DLTcollab/sse2neon | ||
| [torchtree]: https://github.com/4ment/torchtree |
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