C10_fixed — Mixture model

Usage

C10_fixed() → DiscreteDist<CTMC<AA>>

Arguments

This entry has no arguments.

Description

Empirically derived mixture model where different components have different equilibrium frequencies to account for site-specific biochemical constraints. It partitions protein alignment sites into 10 distinct profile classes, each with a unique amino acid distribution, to better approximate the varying selective pressures across a sequence.
This site-heterogeneous approach effectively mitigates long-branch attraction and systematic biases that often compromise simpler, single-matrix models like LG or WAG.
This version fixes the relative frequencies of the 10 components to the values from the paper.

Examples

C10_fixed +> ASRV.Gamma

Citation

Le, Si Quang; Gascuel, Olivier; Lartillot, Nicolas (2008). Phylogenetic mixture models for proteins. Philosophical Transactions of the Royal Society B: Biological Sciences 363(1512): 3965--3976. DOI: 10.1098/rstb.2008.0180

See also