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https://github.com/ms609/treesearch

R package for phylogenetic tree search under custom optimality criteria
https://github.com/ms609/treesearch

bioinformatics morphological-analysis phylogenetics r-package research-tool tree-search

Last synced: 7 days ago
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R package for phylogenetic tree search under custom optimality criteria

Host: GitHub
URL: https://github.com/ms609/treesearch
Owner: ms609
License: gpl-3.0
Created: 2017-07-24T09:09:45.000Z (over 7 years ago)
Default Branch: master
Last Pushed: 2024-05-29T07:38:40.000Z (8 months ago)
Last Synced: 2024-05-29T07:47:21.630Z (8 months ago)
Topics: bioinformatics, morphological-analysis, phylogenetics, r-package, research-tool, tree-search
Language: R
Homepage: https://ms609.github.io/TreeSearch/
Size: 117 MB
Stars: 5
Watchers: 5
Forks: 4
Open Issues: 32
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Codemeta: codemeta.json

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README

        # TreeSearch

  [![codecov](https://codecov.io/gh/ms609/TreeSearch/branch/master/graph/badge.svg)](https://codecov.io/gh/ms609/TreeSearch)

[![CRAN Status Badge](http://www.r-pkg.org/badges/version/TreeSearch)](https://cran.r-project.org/package=TreeSearch)

[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/TreeSearch)](https://cran.r-project.org/package=TreeSearch)

[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/grand-total/TreeSearch)](https://cran.r-project.org/package=TreeSearch)

[![DOI](https://zenodo.org/badge/98171642.svg)](https://zenodo.org/badge/latestdoi/98171642)

[![Project Status: Active – – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

"TreeSearch" (Smith 2023) is an R package that contains a "shiny" user interface for 

interactive tree search and exploration of results, including character

visualization,

[rogue taxon detection](https://ms609.github.io/Rogue) (Smith 2022a),

[tree space mapping](https://ms609.github.io/TreeDist/articles/treespace.html)

(Smith 2022b),

and cluster consensus trees.

Inapplicable character states are handled using the algorithm of Brazeau,

Guillerme and Smith (2019) using the "Morphy" C library (Brazeau _et al_. 2017).

Implied weighting (Goloboff, 1993),

Profile Parsimony (Faith and Trueman, 2001)

and Successive Approximations (Farris, 1969)

are implemented; 

[custom optimality criteria](https://ms609.github.io/TreeSearch/articles/custom.html)

and search approaches can also be defined.

# Installing in R

Full installation instructions, including notes on installing R, are available

in a [vignette](https://ms609.github.io/TreeSearch/articles/getting-started.html).

Install and load the stable version from CRAN as follows:

```r

install.packages("TreeSearch")

library("TreeSearch")

# Launch the Shiny App with:

TreeSearch::EasyTrees()

```

Install and load the development version of "TreeSearch" with:

```r

if(!require("curl")) install.packages("curl")

if(!require("remotes")) install.packages("remotes")

remotes::install_github("ms609/TreeSearch")

library("TreeSearch")

```

# Installing stand-alone application

The TreeSearch user interface can be run as a stand-alone application without

installing R.

[Download](https://github.com/ms609/TreeSearch/releases) the latest release for your platform.

If your preferred platform is not supported, please contact the maintainer.

## Installation on Windows

You may need to obtain the [ffmpeg library](https://community.chocolatey.org/packages/ffmpeg)

before you can run TreeSearch.

This is best installed using ['Chocolatey'](https://chocolatey.org/).

Once chocolatey is installed, open a PowerShell window with administrative privileges, and

type `choco install ffmpeg`; then restart your computer.

# Quick start

Launch a graphical user interface by typing `TreeSearch::EasyTrees()` in the R console.

For more control over search settings, see [`?MaximizeParsimony()`](https://ms609.github.io/TreeSearch/reference/MaximizeParsimony.html).

![Flow charts listing common actions facilitated by TreeSearch](man/figures/Flow.svg)

# Documentation

- [Package functions](https://ms609.github.io/TreeSearch/reference) reference manual

- [Getting started](https://ms609.github.io/TreeSearch/articles/getting-started.html)

- [Using the GUI](https://ms609.github.io/TreeSearch/articles/tree-search.html)

- [Analysing tree spaces](https://ms609.github.io/TreeSearch/articles/tree-space.html)

- [Loading phylogenetic data into R](https://ms609.github.io/TreeTools/articles/load-data.html)

- [Parsimony search with inapplicable data](https://ms609.github.io/TreeSearch/articles/tree-search.html)

- [Calculating concavity profiles](https://ms609.github.io/TreeSearch/articles/profile-scores.html) for Profile Parsimony

- [Tree search with profile parsimony](https://ms609.github.io/TreeSearch/articles/profile.html)

'TreeSearch' uses [semantic versioning](https://semver.org/).

Please note that the 'TreeSearch' project is released with a

[Contributor Code of Conduct](CODE_OF_CONDUCT.md).

By contributing to this project, you agree to abide by its terms.

# References

Brazeau M. D., Smith M. R., Guillerme T. (2017). 

  MorphyLib: a library for phylogenetic analysis of categorical trait data with inapplicability.

  doi: [10.5281/zenodo.815372](https://doi.org/10.5281/zenodo.815372).

Brazeau, M. D., Guillerme, T. and Smith, M. R. (2019).

  An algorithm for morphological phylogenetic analysis with inapplicable data. 

  Systematic Biology, 68(4), 619-631.

  doi: [10.1093/sysbio/syy083](https://dx.doi.org/10.1093/sysbio/syy083).

Faith D. P., Trueman J. W. H. (2001).

  Towards an inclusive philosophy for phylogenetic inference.

  Systematic Biology, 50(3), 331–350. 

  doi: [10.1080/10635150118627](https://doi.org/10.1080/10635150118627).

Farris, J. S. (1969). A successive approximations approach to character weighting. 

  Systematic Biology, 18(4), 374–385.

  doi: [10.2307/2412182](https://dx.doi.org/10.2307/2412182).

Goloboff, P. A. (1993).

  Estimating character weights during tree search.

  Cladistics, 9(1), 83–91.

  doi: [10.1111/j.1096-0031.1993.tb00209.x](https://doi.org/10.1111/j.1096-0031.1993.tb00209.x).

Goloboff, P. A., Torres, A., Arias, J. S. (2018).

  Weighted parsimony outperforms other methods of phylogenetic inference under 

  models appropriate for morphology.

  Cladistics, 34(4), 407–437. doi: [10.1111/cla.12205](https://doi.org/10.1111/cla.12205).

Smith, M. R. (2022a).

  Using information theory to detect rogue taxa and improve phylogenetic trees.

  Systematic Biology, 71(5),  1088–1094.

  doi: [10.1093/sysbio/syab099](https://dx.doi.org/10.1093/sysbio/syab099)

Smith, M. R. (2022b).

  Robust analysis of phylogenetic tree space.

  Systematic Biology, 71(5), 1255–1270.

  doi: [10.1093/sysbio/syab100](https://dx.doi.org/10.1093/sysbio/syab100)

Smith, M. R. (2023).

  TreeSearch: morphological phylogenetic analysis in R.

  R Journal, 14(4), 305-315. doi: [10.32614/RJ-2023-019](https://doi.org/10.32614/RJ-2023-019)