https://github.com/amkram/parsimony-lfs
Science Score: 23.0%
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Repository
Basic Info
- Host: GitHub
- Owner: amkram
- Language: Shell
- Default Branch: master
- Size: 33.6 MB
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- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Online Phylogenetics using Parsimony Supplemental Repository
This repository contains supplemental results, data, and scripts for Thornlow et al., 2022
The subfolders are outlined below.
1_make_starting_tree: This folder contains scripts to produce a filtered global phylogeny, the "starting tree" in the manuscript. Samples from the starting tree are used in 3_real_data_experiments to infer trees from real data.
2_optimize_starting_tree: The starting tree from the previous folder is optimized with various methods, and the best tree is chosen as the "ground truth" over which to simulate sequences (in folder 4_simulated_data_experiments)
3_real_data_experiments: This folder contains scripts and results of tree inference methods on real SARS-CoV-2 data. Each method is compared by log likelihood.
4_simulated_data_experiments: Scripts and results of inference methods on simulated SARS-CoV-2 data. Comparisons between methods are done by computing tree distances to a ground truth phylogeny.
Dependencies
The scripts in this repository use the following programs:
- Python 3
- The UShER suite (UShER, matOptimize, matUtils)
- FastTree 2
- IQ-TREE 2
- RAxML-NG
- TreeCmp
Most of the above can be installed with Conda:
```
Create and activate a new environment
conda create -n parsimony conda activate usher-env
Set up channels
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
Install packages (versions are those used in our experiments except where stated otherwise)
conda install usher=0.4.8 conda install raxml-ng=1.1.0 conda install iqtree=2.1.3 ```
For FastTree 2, install the double-precision executable:
wget http://www.microbesonline.org/fasttree/FastTreeDbl
For TreeCmp, follow the instructions at https://github.com/TreeCmp/TreeCmp
For more details on the UShER suite, see the wiki.
Owner
- Name: Alex Kramer
- Login: amkram
- Kind: user
- Location: Santa Cruz, CA
- Company: @corbett-lab
- Repositories: 45
- Profile: https://github.com/amkram
Graduate student at UC Santa Cruz - Biomolecular Engineering and Bioinformatics
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| Name | Commits | |
|---|---|---|
| Alex Kramer | a****e@u****u | 1 |
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