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https://github.com/starsareintherose/tiger
Identifying rapidly-evolving characters in evolutionary data
https://github.com/starsareintherose/tiger
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Identifying rapidly-evolving characters in evolutionary data
- Host: GitHub
- URL: https://github.com/starsareintherose/tiger
- Owner: starsareintherose
- Created: 2021-06-20T13:28:55.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-01-15T05:22:18.000Z (12 months ago)
- Last Synced: 2024-05-02T03:15:38.241Z (8 months ago)
- Language: Python
- Homepage: http://mcinerneylab.com/software/tiger/
- Size: 384 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# tiger
Identifying rapidly-evolving characters in evolutionary data
## Usage
```
****************
TIGER Help:
****************
TIGER: Tree-Independent Generation of Evolutionary Rates
(Developed by Carla Cummins in the lab of James Mc Inerney, NUI Maynooth, Co. Kildare, Ireland)
-Options:
-in Specify input file. File must be in FastA format and must be aligned prior.
Datasets with uneven sequence lengths will return an error.
-v Returns current TIGER version.
-f Changes output formatting options.
-f s: sorts sites depending on their agreement score
-f r: displays rank values rather than bin numbers
-f s,r: displays sorted ranks (*Be sure to put only a "," NO SPACE!)
Default prints bin numbers unsorted.
-b Set the number of bins to be used.
-b : Sites will be placed into number of bins. is a whole number.
Default is 10
-rl A list of the rate at each site may be optionally written to a specified
file.
-rl : writes list of the rates at each site to file.txt.
-ptp Specifies that a PTP test should be run. *Note: this option has a huge
effect on running time!
-z Number of randomisations to be used for the PTP test.
-z : each site will be randomised times. is a whole number.
Default is 100
-p Specify p-value which denotes significance in PTP test.
-p : site will be denoted as significant if p-value is better than .
is a floating point number.
Default is 0.05
-pl Write a list of p-values to a specified file.
-pl : writes list of p-values for each site to file.txt.
-u Specify unknown characters in the alignment. Unknown characters are omitted from
site patterns and so are not considered in the analysis.
-u ?,-,*: defines ?, - and * as unknown characters. (*Be sure to put only a comma
between characters, NO SPACE!!)
Default is ? only
```
## System Requirements
- Python 3.x.
## Note
Version 1.04 is made by Guoyi Zhang instead of other original authors. So, please cite this repository.
## Citation
- Cummins, C.A. and McInerney, J.O. (2011) A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Systematic Biology 60 (6) 833-844. doi: 10.1093/sysbio/syr064.
- Zhang G. (2022) TIGER version 1.04. https://github.com/starsareintherose/tiger