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