Available rate-heterogeneity options

Site-heterogeneity model types¶

In [1]:

from piqtree import available_rate_type

available_rate_type()

from piqtree import available_rate_type available_rate_type()

Out[1]:

Available rate heterogeneity types

Rate Type	Description
	no invariable sites, no rate heterogeneity model.
I	allowing for a proportion of invariable sites.
G	discrete Gamma model (Yang, 1994) with default 4 rate categories. The number of categories can be changed with e.g. +G8.
I+G	invariable site plus discrete Gamma model (Gu et al., 1995).
R	FreeRate model (Yang, 1995; Soubrier et al., 2012) that generalizes the +G model by relaxing the assumption of Gamma-distributed rates. The number of categories can be specified with e.g. +R6 (default 4 categories if not specified). The FreeRate model typically fits data better than the +G model and is recommended for analysis of large data sets.
I+R	invariable site plus FreeRate model.

6 rows x 2 columns