https://github.com/daviddao/rf-py

Python scripts for extracting and working with bipartitions
https://github.com/daviddao/rf-py

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Python scripts for extracting and working with bipartitions

• Host: GitHub
• URL: https://github.com/daviddao/rf-py
• Owner: daviddao
• Created: 2015-05-27T23:15:13.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2015-07-21T14:38:59.000Z (over 9 years ago)
• Last Synced: 2024-05-01T20:25:47.135Z (7 months ago)
• Language: Python
• Size: 10.9 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# rf-py

RF Opt Algorithm as stand-alone program in Python.

RF-Optimizer is a program for evolutionary analysis of large datasets. 

Given a large evolutionary tree topology, 

it uses a large set of smaller tree topologies to analyse the plausibility of the large tree and proposes corrections as a listing of 

"weak" taxa. A high score for a taxa set stands for low plausibility.

### Dependencies 

- Python3+ 

- bitarray module

- numpy module

### Script dependencies

- Python2.7

- ETE2 

### Current Workflow (will be edited, before production-ready)

- Use RAxML fast plausibility to extract all small bipartitions and induced bipartitions

```ssh

raxmlHPC -f R -m GTRCAT -t largetree -z referencetrees -n T1

```

- This will automatically save the results in a file called bips.txt and the tree names in a file called names.txt

- In rf-opt.py, edit the settings

```python

rf_optimize(starting_tree, end_tree, "path/to/your/raxml-bips")

# Example usage:

rf_optimize(10000, 10020, "bips.txt")

```

- Start the algorithm with

```ssh

python rf-opt.py

```

- All results will be saved in a file called scoring.txt

### Scripts

- read_drops.py takes as input scoring.txt, names.txt and returns you the n best dropsets of this iteration

- reduce_stbase.py takes the trees in stbase and ignores the first n of them (used for testing)

- delete_nodes.py takes a set of trees and deletes a dropset (works currently only with Python2.7 due to ETE dependency)