https://github.com/isaacovercast/pta

Phylogeographic Temporal Analysis
https://github.com/isaacovercast/pta

Last synced: 19 days ago
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Phylogeographic Temporal Analysis

• Host: GitHub
• URL: https://github.com/isaacovercast/pta
• Owner: isaacovercast
• Created: 2019-09-28T03:32:26.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-10-31T15:24:35.000Z (2 months ago)
• Last Synced: 2024-10-31T16:28:42.855Z (2 months ago)
• Language: Jupyter Notebook
• Size: 7.4 MB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 21
• Metadata Files:
  • Readme: README.md

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README

        
# PTA - Phylogeographic Temporal Analysis

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/isaacovercast/PTA/master)

Whole genome or SNP based comparative phylogeographic analysis for co-distributed

assemblages of communities. The result of aggregating a bunch of momis and dadis.

## Quick installation

**PTA requires python 3.9 at the moment.**

* Install [miniconda](https://conda.io/miniconda.html) and activate conda

* Install PTA inside a clean conda environment:

```

conda create -n pta python=3.9

conda activate pta

conda install -c conda-forge -c bioconda -c PTA pta

```

### Stuck solving environment

If the conda install takes a very long time you can try changing the solver to libmamba. If you are impatient you should just do this right away because it works.

```

conda install -n base conda-libmamba-solver

conda config --set solver libmamba

```

Full installation and usage information is available on the [PTA rtfd site](https://pta.readthedocs.io)