Honour user-defined codon frequencies (+FU) for GY-type models - #210
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ModelCodon::init replaced a user-defined frequency type with the model's
default for every mechanistic model. The MG family needs that (its
frequencies are nucleotide-targeted and +FU is turned into F3X4), but
initGY94() returns FREQ_EMPIRICAL, so GY{...}+FU{f1,...,f61} became GY+F:
the 61 values were never read, the report said GY+F with 60 free
parameters and every +FU vector gave the same likelihood. 2.4.0 honoured
the request.
Apply the fallback only when codon_freq_style == CF_TARGET_NT. GY-type
models now keep FREQ_USER_DEFINED, read the frequencies and report +FU
with no free frequency parameters; MG behaviour is unchanged.
Test: test_iqtree.sh/.ps1 run GY+FU with frequencies from
test_data/codon_freq.txt and a GY+F3X4 control on a small codon
alignment; expect_ans.txt carries their log-likelihoods. The +FU row
fails by 26.4 on unmodified master.
Fixes iqtree#192
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TaHntBDKuZJpMAAMenkC44
bqminh
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Sep 10, 2026
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ModelCodon::init replaced a user-defined frequency type with the model's default for every mechanistic model. The MG family needs that (its frequencies are nucleotide-targeted and +FU is turned into F3X4), but initGY94() returns FREQ_EMPIRICAL, so GY{...}+FU{f1,...,f61} became GY+F: the 61 values were never read, the report said GY+F with 60 free parameters and every +FU vector gave the same likelihood. 2.4.0 honoured the request.
Apply the fallback only when codon_freq_style == CF_TARGET_NT. GY-type models now keep FREQ_USER_DEFINED, read the frequencies and report +FU with no free frequency parameters; MG behaviour is unchanged.
Test: test_iqtree.sh/.ps1 run GY+FU with frequencies from test_data/codon_freq.txt and a GY+F3X4 control on a small codon alignment; expect_ans.txt carries their log-likelihoods. The +FU row fails by 26.4 on unmodified master.
Fixes #192
Claude-Session: https://claude.ai/code/session_01TaHntBDKuZJpMAAMenkC44