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traitlab

TraitLab: a Matlab toolbox for fitting and simulating binary tree-like data

https://github.com/traitlab-mcmc/traitlab

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: wiley.com
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    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords

matlab phylogenetics
Last synced: 6 months ago · JSON representation ·

Repository

TraitLab: a Matlab toolbox for fitting and simulating binary tree-like data

Basic Info
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  • Stars: 0
  • Watchers: 2
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Topics
matlab phylogenetics
Created over 9 years ago · Last pushed over 2 years ago
Metadata Files
Readme Citation

README.md

TraitLab

Description

TraitLab implements the stochastic Dollo model for simulating and fitting binary data on trees using Markov chain Monte Carlo methods.

See the TraitLab website for an overview of TraitLab's features and related publications. The manual contains a full description of the tools in TraitLab and a step-by-step tutorial for running an analysis.

Requirements

TraitLab runs in Matlab and requires its Statistics and Machine Learning toolbox.

The TraitLab source code can be downloaded from GitHub, no further installation steps are required unless the borrowing model is being run: see README in the borrowing directory for more details. Please get in touch if you have any issues.

Analysis

TraitLab reads Nexus-formatted data in a .nex file.

A startup file sets up the path when Matlab is started at the top level of the TraitLab directory.

To run an experiment using the GUI:

  • Start Matlab in the TraitLab folder or start Matlab, navigate to the TraitLab folder and execute startup in the Matlab commmand window.
  • Execute TraitLab in the Matlab command window to open the analysis GUI.
  • Load data and set the parameters of the experiments then click start.

TraitLab will write the settings (.par) and output files to the specified directory.

To analyse samples at the end of a run, open the analysis GUI from the toolbar in the main TraitLab GUI.

Alternatively, experiments can be launched from parameter files. matlab batchTraitLab('<path to .par file>'); This allows experiments to be run from the Matlab command window or from the command line.

See the manual for a full description.

Example

The example folder contains a synthetic data set and .par files to run single- and coupled-chain experiments. The README file within describes how to run the experiments.

Owner

  • Name: traitlab-mcmc
  • Login: traitlab-mcmc
  • Kind: organization

Citation (CITATION.cff) 

# YAML 1.2
---
authors:
  - family-names: Kelly
    given-names: "L.J."
    orcid: "https://orcid.org/https://orcid.org/0000-0003-4653-9303"
  - family-names: Nicholls
    given-names: "G.K."
  - family-names: Ryder
    given-names: "R.J."
  - family-names: Welch
    given-names: "D."
cff-version: "1.2.0"
message: "If you use this software, please cite the preferred-citation."
repository-code: "https://github.com/traitlab-mcmc/TraitLab"
title: TraitLab
preferred-citation:
  authors:
  - family-names: "Kelly"
    given-names: "Luke J."
  - family-names: Nicholls
    given-names: "Geoff K."
  - family-names: "Ryder"
    given-names: "Robin J."
  - family-names: "Welch"
    given-names: "David"
  title: "TraitLab: a Matlab package for fitting and simulating binary tree-like data"
  type: article
  year: 2023
  journal: "arXiv:2308.09060"

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