diff --git a/phylo/src/substitution_models/dna_models/gtr.rs b/phylo/src/substitution_models/dna_models/gtr.rs
index 8296b3d..6410e71 100644
--- a/phylo/src/substitution_models/dna_models/gtr.rs
+++ b/phylo/src/substitution_models/dna_models/gtr.rs
@@ -6,17 +6,17 @@ use argmin::solver::brent::BrentOpt;
 use log::info;
 
 use crate::evolutionary_models::EvolutionaryModelInfo;
+use crate::substitution_models::SubstParams;
 use crate::substitution_models::{
     dna_models::{make_dna_model, make_pi, DNASubstModel, DNASubstParams},
     SubstMatrix, SubstitutionLikelihoodCost, SubstitutionModelInfo,
 };
 use crate::Result;
 
-pub fn gtr(model_params: &[f64]) -> Result<DNASubstModel> {
-    let gtr_params = parse_gtr_parameters(model_params)?;
+pub fn gtr(gtr_params: DNASubstParams) -> DNASubstModel {
     info!("Setting up gtr with rates: {}", gtr_params.print_as_gtr());
     let q = gtr_q(&gtr_params);
-    Ok(make_dna_model(gtr_params, q))
+    make_dna_model(gtr_params, q)
 }
 
 pub fn parse_gtr_parameters(model_params: &[f64]) -> Result<DNASubstParams> {
@@ -86,7 +86,7 @@ fn gtr_q(gtr: &DNASubstParams) -> SubstMatrix {
 
 impl DNASubstModel {
     pub(crate) fn reset_gtr(&mut self, params: &DNASubstParams) {
-        self.params = ((*params).clone()).into();
+        self.params = SubstParams::DNA((*params).clone());
         self.q = gtr_q(params);
     }
 }
@@ -116,7 +116,9 @@ impl CostFunction for GTRParamOptimiser<'_> {
     type Output = f64;
 
     fn cost(&self, param: &Self::Param) -> Result<Self::Output> {
-        let mut params = parse_gtr_parameters(self.base_model.params.as_slice())?;
+        let SubstParams::DNA(mut params) = self.base_model.params.clone() else {
+            unreachable!()
+        };
         match self.parameter {
             ParamEnum::Pit | ParamEnum::Pic | ParamEnum::Pia | ParamEnum::Pig => {
                 bail!("Cannot optimise frequencies for now.")
@@ -158,13 +160,7 @@ impl<'a> GTRModelOptimiser<'a> {
     }
 
     pub fn optimise_parameters(&self) -> Result<(u32, DNASubstParams, f64)> {
-        let epsilon = 1e-10;
-        let params = self.base_model.params.clone();
-        let model = gtr(params.as_slice())?;
-        let mut logl = f64::NEG_INFINITY;
-        let mut new_logl = 0.0;
-        let mut gtr_params = parse_gtr_parameters(params.as_slice())?;
-        let mut iters = 0;
+        let epsilon = 1e-5;
         let params_to_optimise = [
             ParamEnum::Rag,
             ParamEnum::Rca,
@@ -173,6 +169,14 @@ impl<'a> GTRModelOptimiser<'a> {
             ParamEnum::Rtc,
             ParamEnum::Rtg,
         ];
+        let SubstParams::DNA(mut gtr_params) = self.base_model.params.clone() else {
+            unreachable!()
+        };
+        let model = gtr(gtr_params.clone());
+        let mut logl = f64::NEG_INFINITY;
+        let mut new_logl = 0.0;
+        let mut iters = 0;
+
         while (logl - new_logl).abs() > epsilon {
             println!("Iteration: {}", iters);
             logl = new_logl;
@@ -226,7 +230,7 @@ mod gtr_optimisation_tests {
     fn check_parameter_optimisation_gtr() {
         // Original params from paml: 0.88892  0.03190  0.00001  0.07102  0.02418
         let info = phyloinfo_from_files(
-            PathBuf::from("./data/sim/gtr/gtr.fasta"),
+            PathBuf::from("./data/sim/GTR/gtr.fasta"),
             PathBuf::from("./data/sim/tree.newick"),
         )
         .unwrap();
@@ -242,7 +246,7 @@ mod gtr_optimisation_tests {
         let mut tmp_info = SubstitutionModelInfo::new(likelihood.info, &model).unwrap();
         let unopt_logl = likelihood.compute_log_likelihood(&model, &mut tmp_info);
         assert_relative_eq!(unopt_logl, -3474.48083, epsilon = 1.0e-5);
-        let (iters, params, logl) = GTRModelOptimiser::new(&likelihood, &model)
+        let (_, _, logl) = GTRModelOptimiser::new(&likelihood, &model)
             .optimise_parameters()
             .unwrap();
         assert!(logl > unopt_logl);
diff --git a/phylo/src/substitution_models/dna_models/hky.rs b/phylo/src/substitution_models/dna_models/hky.rs
index 8f4d34b..41faf43 100644
--- a/phylo/src/substitution_models/dna_models/hky.rs
+++ b/phylo/src/substitution_models/dna_models/hky.rs
@@ -7,14 +7,13 @@ use crate::substitution_models::dna_models::{
 use crate::substitution_models::FreqVector;
 use crate::Result;
 
-pub fn hky(model_params: &[f64]) -> Result<DNASubstModel> {
-    let hky_params = parse_hky_parameters(model_params)?;
+pub fn hky(hky_params: DNASubstParams) -> DNASubstModel {
     info!(
         "Setting up hky with parameters {}",
         hky_params.print_as_hky()
     );
     let q = tn93_q(&hky_params);
-    Ok(make_dna_model(hky_params, q))
+    make_dna_model(hky_params, q)
 }
 
 pub fn parse_hky_parameters(model_params: &[f64]) -> Result<DNASubstParams> {
diff --git a/phylo/src/substitution_models/dna_models/jc69.rs b/phylo/src/substitution_models/dna_models/jc69.rs
index cf6c7b6..0ec96ce 100644
--- a/phylo/src/substitution_models/dna_models/jc69.rs
+++ b/phylo/src/substitution_models/dna_models/jc69.rs
@@ -6,13 +6,12 @@ use crate::substitution_models::{
 };
 use crate::Result;
 
-pub fn jc69(model_params: &[f64]) -> Result<DNASubstModel> {
-    let jc69_params = parse_jc69_parameters(model_params)?;
+pub fn jc69(jc69_params: DNASubstParams) -> DNASubstModel {
     info!(
         "Setting up jc69 with parameters: {}",
         jc69_params.print_as_jc69()
     );
-    Ok(make_dna_model(jc69_params, jc69_q()))
+    make_dna_model(jc69_params, jc69_q())
 }
 
 pub fn parse_jc69_parameters(model_params: &[f64]) -> Result<DNASubstParams> {
diff --git a/phylo/src/substitution_models/dna_models/k80.rs b/phylo/src/substitution_models/dna_models/k80.rs
index 1b58ea6..df34ad1 100644
--- a/phylo/src/substitution_models/dna_models/k80.rs
+++ b/phylo/src/substitution_models/dna_models/k80.rs
@@ -1,24 +1,25 @@
 use std::ops::Div;
 
+use anyhow::bail;
 use argmin::core::{CostFunction, Executor};
 use argmin::solver::brent::BrentOpt;
 use log::{info, warn};
 
 use crate::evolutionary_models::EvolutionaryModelInfo;
+use crate::substitution_models::SubstParams;
 use crate::substitution_models::{
     dna_models::{dna_substitution_parameters::DNASubstParams, make_dna_model, DNASubstModel},
     FreqVector, SubstMatrix, SubstitutionLikelihoodCost, SubstitutionModelInfo,
 };
 use crate::Result;
 
-pub fn k80(model_params: &[f64]) -> Result<DNASubstModel> {
-    let k80_params = parse_k80_parameters(model_params)?;
+pub fn k80(k80_params: DNASubstParams) -> DNASubstModel {
     info!(
         "Setting up k80 with parameters: {}",
         k80_params.print_as_k80()
     );
     let q = k80_q(&k80_params);
-    Ok(make_dna_model(k80_params, q))
+    make_dna_model(k80_params, q)
 }
 
 pub fn parse_k80_parameters(model_params: &[f64]) -> Result<DNASubstParams> {
@@ -80,9 +81,9 @@ pub fn k80_q(p: &DNASubstParams) -> SubstMatrix {
 }
 
 impl DNASubstModel {
-    pub(crate) fn reset_k80_q(&mut self, params: &DNASubstParams) {
-        self.params = ((*params).clone()).into();
-        self.q = k80_q(params);
+    pub(crate) fn reset_k80_q(&mut self, params: DNASubstParams) {
+        self.q = k80_q(&params);
+        self.params = SubstParams::DNA(params);
     }
 }
 
@@ -114,12 +115,12 @@ impl<'a> K80ModelOptimiser<'a> {
 
     pub fn optimise_parameters(&self) -> Result<(u32, DNASubstParams, f64)> {
         let epsilon = 1e-10;
-        let alpha = self.base_model.params[0];
-        let beta = self.base_model.params[1];
-        let mut model = k80(&[alpha, beta])?;
+        let SubstParams::DNA(mut k80_params) = self.base_model.params.clone() else {
+            unreachable!();
+        };
+        let mut model = k80(k80_params.clone());
         let mut logl = f64::NEG_INFINITY;
         let mut new_logl = 0.0;
-        let mut k80_params = k80_params(alpha, beta);
         let mut iters = 0;
         while (logl - new_logl).abs() > epsilon {
             logl = new_logl;
@@ -135,7 +136,7 @@ impl<'a> K80ModelOptimiser<'a> {
         model: &mut DNASubstModel,
         k80_params: &mut DNASubstParams,
     ) -> Result<f64> {
-        model.reset_k80_q(k80_params);
+        model.reset_k80_q(k80_params.clone());
         let alpha_optimiser = K80ModelAlphaOptimiser {
             likelihood_cost: self.likelihood_cost,
             base_model: model,
@@ -152,7 +153,7 @@ impl<'a> K80ModelOptimiser<'a> {
         model: &mut DNASubstModel,
         k80_params: &mut DNASubstParams,
     ) -> Result<f64> {
-        model.reset_k80_q(k80_params);
+        model.reset_k80_q(k80_params.clone());
         let beta_optimiser = K80ModelBetaOptimiser {
             likelihood_cost: self.likelihood_cost,
             base_model: model,
@@ -177,7 +178,12 @@ impl CostFunction for K80ModelAlphaOptimiser<'_> {
 
     fn cost(&self, param: &Self::Param) -> Result<Self::Output> {
         let mut model = self.base_model.clone();
-        model.reset_k80_q(&k80_params(*param, self.base_model.params[1]));
+        let SubstParams::DNA(mut k80_params) = model.params.clone() else {
+            bail!("Incorrect substitution model parameter type.")
+        };
+        k80_params.rtc = *param;
+        k80_params.rag = *param;
+        model.reset_k80_q(k80_params);
         let mut tmp_info = SubstitutionModelInfo::new(self.likelihood_cost.info, &model)?;
         Ok(-self
             .likelihood_cost
@@ -195,7 +201,14 @@ impl CostFunction for K80ModelBetaOptimiser<'_> {
 
     fn cost(&self, param: &Self::Param) -> Result<Self::Output> {
         let mut model = self.base_model.clone();
-        model.reset_k80_q(&k80_params(self.base_model.params[0], *param));
+        let SubstParams::DNA(mut k80_params) = model.params.clone() else {
+            bail!("Incorrect substitution model parameter type.")
+        };
+        k80_params.rta = *param;
+        k80_params.rtg = *param;
+        k80_params.rca = *param;
+        k80_params.rcg = *param;
+        model.reset_k80_q(k80_params);
         let mut tmp_info = SubstitutionModelInfo::new(self.likelihood_cost.info, &model)?;
         Ok(-self
             .likelihood_cost
diff --git a/phylo/src/substitution_models/dna_models/mod.rs b/phylo/src/substitution_models/dna_models/mod.rs
index 98be91c..6d40636 100644
--- a/phylo/src/substitution_models/dna_models/mod.rs
+++ b/phylo/src/substitution_models/dna_models/mod.rs
@@ -9,8 +9,8 @@ use crate::evolutionary_models::{EvolutionaryModel, EvolutionaryModelInfo};
 use crate::likelihood::LikelihoodCostFunction;
 use crate::sequences::{charify, dna_alphabet, AMBIG, NUCLEOTIDES_STR};
 use crate::substitution_models::{
-    FreqVector, ParsimonyModel, SubstMatrix, SubstitutionLikelihoodCost, SubstitutionModel,
-    SubstitutionModelInfo,
+    FreqVector, ParsimonyModel, SubstMatrix, SubstParams, SubstitutionLikelihoodCost,
+    SubstitutionModel, SubstitutionModelInfo,
 };
 use crate::{Result, Rounding};
 
@@ -61,13 +61,10 @@ fn dna_ambiguous_chars() -> HashMap<u8, HashSet<u8>> {
     }
 }
 
-fn make_dna_model(
-    params: dna_substitution_parameters::DNASubstParams,
-    q: SubstMatrix,
-) -> DNASubstModel {
+fn make_dna_model(params: DNASubstParams, q: SubstMatrix) -> DNASubstModel {
     let pi = params.pi.clone();
     DNASubstModel {
-        params: params.into(),
+        params: SubstParams::DNA(params),
         index: nucleotide_index(),
         q,
         pi,
@@ -80,11 +77,11 @@ impl EvolutionaryModel<4> for DNASubstModel {
         Self: std::marker::Sized,
     {
         match model_name.to_uppercase().as_str() {
-            "JC69" => jc69(model_params),
-            "K80" => k80(model_params),
-            "HKY" => hky(model_params),
-            "TN93" => tn93(model_params),
-            "GTR" => gtr(model_params),
+            "JC69" => Ok(jc69(parse_jc69_parameters(model_params)?)),
+            "K80" => Ok(k80(parse_k80_parameters(model_params)?)),
+            "HKY" => Ok(hky(parse_hky_parameters(model_params)?)),
+            "TN93" => Ok(tn93(parse_tn93_parameters(model_params)?)),
+            "GTR" => Ok(gtr(parse_gtr_parameters(model_params)?)),
             _ => bail!("Unknown DNA model requested."),
         }
     }
diff --git a/phylo/src/substitution_models/dna_models/tn93.rs b/phylo/src/substitution_models/dna_models/tn93.rs
index fa80e7e..e35541a 100644
--- a/phylo/src/substitution_models/dna_models/tn93.rs
+++ b/phylo/src/substitution_models/dna_models/tn93.rs
@@ -12,14 +12,13 @@ use crate::substitution_models::{
 };
 use crate::Result;
 
-pub fn tn93(model_params: &[f64]) -> Result<DNASubstModel> {
-    let tn93_params = parse_tn93_parameters(model_params)?;
+pub fn tn93(tn93_params: DNASubstParams) -> DNASubstModel {
     info!(
         "Setting up tn93 with parameters {}",
         tn93_params.print_as_tn93()
     );
     let q = tn93_q(&tn93_params);
-    Ok(make_dna_model(tn93_params, q))
+    make_dna_model(tn93_params, q)
 }
 
 pub fn parse_tn93_parameters(model_params: &[f64]) -> Result<DNASubstParams> {
diff --git a/phylo/src/substitution_models/mod.rs b/phylo/src/substitution_models/mod.rs
index 55b477d..1704c9a 100644
--- a/phylo/src/substitution_models/mod.rs
+++ b/phylo/src/substitution_models/mod.rs
@@ -16,10 +16,16 @@ pub mod protein_models;
 pub type SubstMatrix = DMatrix<f64>;
 pub type FreqVector = DVector<f64>;
 
+#[derive(Clone, Debug, PartialEq)]
+pub enum SubstParams {
+    DNA(dna_models::DNASubstParams),
+    Protein(protein_models::ProteinSubstParams),
+}
+
 #[derive(Clone, Debug, PartialEq)]
 pub struct SubstitutionModel<const N: usize> {
     index: [i32; 255],
-    pub params: Vec<f64>,
+    pub params: SubstParams,
     pub(crate) q: SubstMatrix,
     pub(crate) pi: FreqVector,
 }
diff --git a/phylo/src/substitution_models/protein_models.rs b/phylo/src/substitution_models/protein_models.rs
index 5fc947c..19cb007 100644
--- a/phylo/src/substitution_models/protein_models.rs
+++ b/phylo/src/substitution_models/protein_models.rs
@@ -8,8 +8,8 @@ use crate::evolutionary_models::EvolutionaryModel;
 use crate::likelihood::LikelihoodCostFunction;
 use crate::sequences::{charify, AMINOACIDS_STR};
 use crate::substitution_models::{
-    FreqVector, ParsimonyModel, SubstMatrix, SubstitutionLikelihoodCost, SubstitutionModel,
-    SubstitutionModelInfo,
+    FreqVector, ParsimonyModel, SubstMatrix, SubstParams, SubstitutionLikelihoodCost,
+    SubstitutionModel, SubstitutionModelInfo,
 };
 use crate::{Result, Rounding};
 
@@ -20,6 +20,11 @@ pub type ProteinSubstModel = SubstitutionModel<20>;
 pub type ProteinLikelihoodCost<'a> = SubstitutionLikelihoodCost<'a, 20>;
 pub type ProteinSubstModelInfo = SubstitutionModelInfo<20>;
 
+#[derive(Clone, Debug, PartialEq)]
+pub struct ProteinSubstParams {
+    pub(crate) pi: FreqVector,
+}
+
 impl ProteinSubstModel {
     fn normalise(&mut self) {
         let factor = -(self.pi.transpose() * self.q.diagonal())[(0, 0)];
@@ -39,7 +44,7 @@ impl EvolutionaryModel<20> for ProteinSubstModel {
             _ => bail!("Unknown protein model requested."),
         };
         let mut model = ProteinSubstModel {
-            params: vec![],
+            params: SubstParams::Protein(ProteinSubstParams { pi: pi.clone() }),
             index: aminoacid_index(),
             q,
             pi,