RateCounter
RateCounter is a python library and program for calculating the number of rate differences between taxa given a nexus file.
It is based on the method in:
Greenhill SJ, Hua X, Welsh CF, Schneemann H & Bromham L. 2018. [Population Size and the Rate of Language Evolution: A Test across Indo-European, Austronesian and Bantu Languages](https://www.frontiersin.org/articles/10.3389/fpsyg.2018.00576/abstract). Frontiers in Psychology doi: 10.3389/fpsyg.2018.00576
Please cite this paper if you find this software helpful.
Installation:
pip install RateCounterUsage:
As a standalone program:
> ratecounter --help
usage: ratecounter [-h] [-v] nexus taxon1 taxon2
Calculate rates from the nexus for the two taxa
positional arguments:
nexus nexusfile
taxon1 Taxon 1
taxon2 Taxon 2
optional arguments:
-h, --help show this help message and exit
-v, --verbose increases verbosity
> ratecounter test.nex Taxon1 Taxon2
GAIN A 1
GAIN B 1
LOSS A 1
LOSS B 1
TOTAL A 2
TOTAL B 2
ABSENCE 1
RETENTION 1
SHARED GAIN 1
SHARED LOSS 1
UNCOUNTABLE 19
TOTAL 27As a python library
from ratecounter.main import RateCounter
rc = RateCounter(nexusfile=args.nexusfile)
scores = rc.get_scores(Taxon1, Taxon2)
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