76 lines
2.6 KiB
Markdown
76 lines
2.6 KiB
Markdown
# 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 <int>: Sites will be placed into <int> number of bins. <int> 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 <file.txt> : 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 <int>: each site will be randomised <int> times. <int> is a whole number.
|
|
|
|
Default is 100
|
|
|
|
-p Specify p-value which denotes significance in PTP test.
|
|
-p <float>: site will be denoted as significant if p-value is better than <float>.
|
|
<float> is a floating point number.
|
|
|
|
Default is 0.05
|
|
|
|
-pl Write a list of p-values to a specified file.
|
|
-pl <file.txt>: 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
|