diff --git a/config/demog/ArchIE_4D19.yaml b/config/demog/ArchIE_4D19.yaml
deleted file mode 100644
index d84a02e..0000000
--- a/config/demog/ArchIE_4D19.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
-doi:
-    - https://doi.org/10.1371/journal.pgen.1008175
-time_units: generations
-demes:
-    - name: Anc
-      epochs:
-          - {end_time: 2500, start_size: 10000}
-    - name: Ghost
-      ancestors: [Anc]
-      start_time: 12000
-      epochs: # https://github.com/sriramlab/ArchIE/blob/master/simulations/ms.sh#L7C48-L7C179
-          - {end_time: 6120, start_size: 10000}
-          - {end_time: 6000, start_size: 100}
-          - {end_time: 0, start_size: 10000}
-    - name: Ref
-      ancestors: [Anc]
-      epochs:
-          - {end_time: 0, start_size: 10000}
-    - name: Tgt
-      ancestors: [Anc]
-      epochs:
-          - {end_time: 0, start_size: 10000}
-    - name: Unused
-      ancestors: [Ghost]
-      start_time: 7000
-      epochs:
-          - {end_time: 0, start_size: 10000}
-pulses:
-    - {sources: [Ghost], dest: Tgt, time: 2000, proportions: [0.02]}
diff --git a/config/demog/HumanNeanderthal_3G21.yaml b/config/demog/HumanNeanderthal_3G21.yaml
deleted file mode 100644
index 112c054..0000000
--- a/config/demog/HumanNeanderthal_3G21.yaml
+++ /dev/null
@@ -1,30 +0,0 @@
-# Human-Neantherthal introgression model
-description:
-  A composite hominin model with demographic parameters taken from
-  Gower et al. (2021).
-
-time_units: generations
-
-doi:
-- https://doi.org/10.7554/eLife.64669
-
-demes:
-    - name: Anc
-      epochs:
-          - {end_time: 2265.5172413793102, start_size: 18500.0}
-    - name: Nea
-      ancestors: [Anc]
-      start_time: 18965.51724137931
-      epochs:
-          - {end_time: 0, start_size: 3400.0}
-    - name: CEU
-      ancestors: [Anc]
-      epochs:
-          - {end_time: 1100.0, start_size: 1080.0}
-          - {start_size: 1450.0, end_size: 13377.357734109575}
-    - name: YRI
-      ancestors: [Anc]
-      epochs:
-          - {end_time: 0, start_size: 27000.0}
-pulses:
-    - {sources: [Nea], dest: CEU, time: 1896.551724137931, proportions: [0.0225]}
diff --git a/config/features/archie.features.yaml b/config/features/archie.features.yaml
deleted file mode 100644
index 7dd97a1..0000000
--- a/config/features/archie.features.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-features: 
-    reference distances:
-        minimum:
-    target distances:
-        all:
-        mean:
-        variance:
-        skew:
-        kurtosis:
-    individual allele frequency spectra:
-    number of private mutations:
-    sstar:
-        genotype distance: 'archie'
-        match bonus: 5000
-        max mismatch: 5
-        mismatch penalty: -10000
diff --git a/config/scenarios/config1.yaml b/config/scenarios/config1.yaml
deleted file mode 100644
index 1fd4140..0000000
--- a/config/scenarios/config1.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-seed: 12345
-feature_id: "archie"
-feature_config: "config/features/archie.features.yaml"
-nfeature: 1000000
-nref: 108
-ntgt: 50
-ploidy: 2
-geno_states: ["phased", "unphased"]
-output_prefix: "gita.lr.archie.config1"
-
-nrep:
-    train: 10
-    test: 10
-
-seq_len: 
-    train: 50000
-    test: 200000000
-
-demog_id: 
-    train: "HumanNeanderthal_3G21"
-    test: "HumanNeanderthal_3G21"
-
-demes: 
-    train: "config/demog/HumanNeanderthal_3G21.yaml"
-    test: "config/demog/HumanNeanderthal_3G21.yaml"
-
-mut_rate: 
-    train: 1.29e-8
-    test: 1.29e-8
-
-rec_rate: 
-    train: 1e-8
-    test: 1e-8
-
-ref_id: 
-    train: "YRI"
-    test: "YRI"
-
-tgt_id:
-    train: "CEU"
-    test: "CEU"
-
-src_id: 
-    train: "Nea"
-    test: "Nea"
-
-win_step: 10000
-cutoff_num: 20
diff --git a/config/scenarios/config2.yaml b/config/scenarios/config2.yaml
deleted file mode 100644
index 76fbf38..0000000
--- a/config/scenarios/config2.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-seed: 12345
-feature_id: "archie"
-feature_config: "config/features/archie.features.yaml"
-nfeature: 1000000
-nref: 50
-ntgt: 50
-ploidy: 2
-geno_states: ["phased", "unphased"]
-output_prefix: "gita.lr.archie.config2"
-
-nrep:
-    train: 10
-    test: 10
-
-seq_len: 
-    train: 50000
-    test: 200000000
-
-demog_id: 
-    train: "ArchIE_4D19"
-    test: "HumanNeanderthal_3G21"
-
-demes: 
-    train: "config/demog/ArchIE_4D19.yaml"
-    test: "config/demog/HumanNeanderthal_3G21.yaml"
-
-mut_rate: 
-    train: 1.25e-8
-    test: 1.29e-8
-
-rec_rate: 
-    train: 1e-8
-    test: 1e-8
-
-ref_id: 
-    train: "Ref"
-    test: "YRI"
-
-tgt_id:
-    train: "Tgt"
-    test: "CEU"
-
-src_id: 
-    train: "Ghost"
-    test: "Nea"
-
-win_step: 10000
-cutoff_num: 20 
diff --git a/config/scenarios/config3.yaml b/config/scenarios/config3.yaml
deleted file mode 100644
index b06fef3..0000000
--- a/config/scenarios/config3.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-seed: 12345
-feature_id: "archie"
-feature_config: "config/features/archie.features.yaml"
-nfeature: 1000000
-nref: 50
-ntgt: 50
-ploidy: 2
-geno_states: ["phased", "unphased"]
-output_prefix: "gita.lr.archie.config3"
-
-nrep:
-    train: 10
-    test: 10
-
-seq_len: 
-    train: 50000
-    test: 200000000
-
-demog_id: 
-    train: "HumanNeanderthal_3G21"
-    test: "HumanNeanderthal_3G21"
-
-demes: 
-    train: "config/demog/HumanNeanderthal_3G21.yaml"
-    test: "config/demog/HumanNeanderthal_3G21.yaml"
-
-mut_rate: 
-    train: 1.29e-8
-    test: 1.29e-8
-
-rec_rate: 
-    train: 1e-8
-    test: 1e-8
-
-ref_id: 
-    train: "YRI"
-    test: "YRI"
-
-tgt_id:
-    train: "CEU"
-    test: "CEU"
-
-src_id: 
-    train: "Nea"
-    test: "Nea"
-
-win_step: 10000
-cutoff_num: 20
diff --git a/config/scenarios/config4.yaml b/config/scenarios/config4.yaml
deleted file mode 100644
index f3c437a..0000000
--- a/config/scenarios/config4.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-seed: 12345
-feature_id: "archie"
-feature_config: "config/features/archie.features.yaml"
-nfeature: 1000000
-nref: 50
-ntgt: 50
-ploidy: 2
-geno_states: ["phased", "unphased"]
-output_prefix: "gita.lr.archie.config4"
-
-nrep:
-    train: 10
-    test: 10
-
-seq_len: 
-    train: 50000
-    test: 200000000
-
-demog_id: 
-    train: "ArchIE_4D19"
-    test: "ArchIE_4D19"
-
-demes: 
-    train: "config/demog/ArchIE_4D19.yaml"
-    test: "config/demog/ArchIE_4D19.yaml"
-
-mut_rate: 
-    train: 1.25e-8
-    test: 1.25e-8
-
-rec_rate: 
-    train: 1e-8
-    test: 1e-8
-
-ref_id: 
-    train: "Ref"
-    test: "Ref"
-
-tgt_id:
-    train: "Tgt"
-    test: "Tgt"
-
-src_id: 
-    train: "Ghost"
-    test: "Ghost"
-
-win_step: 10000
-cutoff_num: 20 
diff --git a/config/scenarios/config5.yaml b/config/scenarios/config5.yaml
deleted file mode 100644
index 2310cae..0000000
--- a/config/scenarios/config5.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-seed: 12345
-feature_id: "archie"
-feature_config: "config/features/archie.features.yaml"
-nfeature: 1000000
-nref: 50
-ntgt: 50
-ploidy: 2
-geno_states: ["phased", "unphased"]
-output_prefix: "gita.lr.archie.config5"
-
-nrep:
-    train: 10
-    test: 10
-
-seq_len: 
-    train: 50000
-    test: 200000000
-
-demog_id: 
-    train: "HumanNeanderthal_3G21"
-    test: "ArchIE_4D19"
-
-demes: 
-    train: "config/demog/HumanNeanderthal_3G21.yaml"
-    test: "config/demog/ArchIE_4D19.yaml"
-
-mut_rate: 
-    train: 1.29e-8
-    test: 1.25e-8
-
-rec_rate: 
-    train: 1e-8
-    test: 1e-8
-
-ref_id: 
-    train: "YRI"
-    test: "Ref"
-
-tgt_id:
-    train: "CEU"
-    test: "Tgt"
-
-src_id: 
-    train: "Nea"
-    test: "Ghost"
-
-win_step: 10000
-cutoff_num: 20 
diff --git a/config/scenarios/config6.yaml b/config/scenarios/config6.yaml
deleted file mode 100644
index a18cecf..0000000
--- a/config/scenarios/config6.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-seed: 12345
-feature_id: "archie"
-feature_config: "config/features/archie.features.yaml"
-nfeature: 10000000
-nref: 50
-ntgt: 50
-ploidy: 2
-geno_states: ["phased", "unphased"]
-output_prefix: "gita.lr.archie.config6"
-
-nrep:
-    train: 10
-    test: 10
-
-seq_len: 
-    train: 50000
-    test: 200000000
-
-demog_id: 
-    train: "ArchIE_4D19"
-    test: "ArchIE_4D19"
-
-demes: 
-    train: "config/demog/ArchIE_4D19.yaml"
-    test: "config/demog/ArchIE_4D19.yaml"
-
-mut_rate: 
-    train: 1.25e-8
-    test: 1.25e-8
-
-rec_rate: 
-    train: 1e-8
-    test: 1e-8
-
-ref_id: 
-    train: "Ref"
-    test: "Ref"
-
-tgt_id:
-    train: "Tgt"
-    test: "Tgt"
-
-src_id: 
-    train: "Ghost"
-    test: "Ghost"
-
-win_step: 10000
-cutoff_num: 20 
diff --git a/workflow/envs/sai.yaml b/workflow/envs/sai.yaml
new file mode 100644
index 0000000..dd8af4d
--- /dev/null
+++ b/workflow/envs/sai.yaml
@@ -0,0 +1,13 @@
+name: sai
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - natsort=8.4.0
+  - numpy=1.26.4
+  - pandas=2.2.1
+  - pydantic=2.11.7
+  - pysam=0.23.0
+  - python=3.9.19
+  - scikit-allel=1.3.7
+  - scipy=1.12.0
diff --git a/workflow/rules/commons/plot.smk b/workflow/rules/commons/plot.smk
deleted file mode 100644
index db10dba..0000000
--- a/workflow/rules/commons/plot.smk
+++ /dev/null
@@ -1,11 +0,0 @@
-rule plot:
-    input:
-        performance = rules.summary.output.summary,
-    output:
-        png = "results/plots/{output_prefix}.performance.png",
-    log:
-        "logs/plot/{output_prefix}.log",
-    resources:
-        partition = "himem,gpu",
-    script:
-        "../scripts/plot.py"
diff --git a/workflow/rules/commons/simulation.smk b/workflow/rules/commons/simulation.smk
deleted file mode 100644
index 1676f7f..0000000
--- a/workflow/rules/commons/simulation.smk
+++ /dev/null
@@ -1,131 +0,0 @@
-rule simulate_test_data:
-    input:
-        demes_file = demes["test"],
-    output:
-        ts = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.ts",
-        vcf = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.vcf",
-        ref = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.ref.ind.list",
-        tgt = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.tgt.ind.list",
-    log:
-        "logs/simulate_test_data/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.log",
-    resources:
-        partition = "himem,gpu",
-    params:
-        ploidy = ploidy,
-        seq_len = seq_len["test"],
-        mut_rate = mut_rate["test"],
-        rec_rate = rec_rate["test"],
-        ref_id = ref_id["test"],
-        tgt_id = tgt_id["test"],
-        src_id = src_id["test"],
-    script:
-        "../scripts/simulation.py"
-
-
-rule compress_vcf:
-    input:
-        vcf = rules.simulate_test_data.output.vcf,
-    output:
-        vcf = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.vcf.gz",
-    log:
-        "logs/compress_vcf/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.log",
-    resources:
-        partition = "himem,gpu",
-    shell:
-        """
-        bgzip -c {input.vcf} > {output.vcf} 2> {log}
-        tabix -p vcf {output.vcf} 2>> {log}
-        rm {input.vcf} 2>> {log}
-        """
-
-
-rule get_phased_true_tracts:
-    input:
-        ts = rules.simulate_test_data.output.ts,
-    output:
-        bed = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.phased.true.tracts.bed",
-    log:
-        "logs/get_phased_true_tracts/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.log",
-    params:
-        ploidy = ploidy,
-        tgt_id = tgt_id["test"],
-        src_id = src_id["test"],
-    resources:
-        partition = "himem", 
-        time = 60, 
-        mem_gb = 2000, 
-        cpus = 128,
-    run:
-        import tskit
-        import pyranges as pr
-        from multiprocessing import Process, Manager
-
-        def worker_func(in_queue, out_queue, **kwargs):
-            while True:
-                trees, migration = in_queue.get()
-                tgt_name = kwargs['tgt_name']
-                ts = kwargs['ts']
-                ploidy = kwargs['ploidy']
-
-                res = ''
-
-                try:
-                    for t in trees:
-                        for n in ts.samples(tgt_name):
-                            if t.is_descendant(n, migration.node):
-                                 left = migration.left if migration.left > t.interval.left else t.interval.left
-                                 right = migration.right if migration.right < t.interval.right else t.interval.right
-                                 res += f'1\t{int(left)}\t{int(right)}\ttsk_{ts.node(n).individual}_{int(n%ploidy+1)}\n'
-                    out_queue.put(res)
-                except Exception as e:
-                # Handle or log the exception as needed
-                    print(f"Error in worker: {e}")
-
-        ts = tskit.load(input.ts)
-
-        src_name = [p.id for p in ts.populations() if p.metadata['name']==params.src_id][0]
-        tgt_name = [p.id for p in ts.populations() if p.metadata['name']==params.tgt_id][0]
-
-        res = "Chromosome\tStart\tEnd\tSample\n"
-        with Manager() as manager:
-            in_queue  = manager.Queue()
-            out_queue = manager.Queue()
-            keywords = {'tgt_name': tgt_name, 'ts': ts, 'ploidy': params.ploidy}
-            workers = [
-                Process(target=worker_func, args=(in_queue, out_queue), kwargs=keywords) for i in range(resources.cpus)
-            ]
-
-            num_introgression = 0
-
-            for m in ts.migrations():
-                if (m.dest==src_name) and (m.source==tgt_name):
-                    in_queue.put((ts.trees(left=m.left, right=m.right), m))
-                    num_introgression += 1
-
-            for w in workers: w.start()
-
-            try:
-                for i in range(num_introgression):
-                    item = out_queue.get()
-                    res += item
-                for w in workers: w.terminate()
-            except Exception as e:
-                print(f"Error in manager: {e}")
-
-        res = pr.from_string(res)
-        res = res.merge(strand=False, by='Sample')
-        if not res.empty: res.to_csv(output.bed, sep="\t", header=False)
-        else: open(output.bed, 'w').close()
-
-
-rule get_unphased_true_tracts:
-    input:
-        bed = rules.get_phased_true_tracts.output.bed,
-    output:
-        bed = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.unphased.true.tracts.bed",
-    log:
-        "logs/get_unphased_true_tracts/{test_demog}/nref_{nref}/ntgt_{ntgt}/{test_seed}/{output_prefix}.log",
-    resources:
-        partition = "himem,gpu",
-    script:
-        "../scripts/get_unphased_true_tracts.py"
diff --git a/workflow/rules/methods/lr/apply.gita.lr.smk b/workflow/rules/methods/lr/apply.gita.lr.smk
deleted file mode 100644
index 0a00386..0000000
--- a/workflow/rules/methods/lr/apply.gita.lr.smk
+++ /dev/null
@@ -1,2 +0,0 @@
-rule process_real_data:
-rule apply_logistic_regression_model:
diff --git a/workflow/rules/methods/lr/test.gita.lr.smk b/workflow/rules/methods/lr/test.gita.lr.smk
deleted file mode 100644
index 9985c1c..0000000
--- a/workflow/rules/methods/lr/test.gita.lr.smk
+++ /dev/null
@@ -1,93 +0,0 @@
-rule process_test_data:
-    input:
-        vcf = rules.compress_vcf.output.vcf,
-        ref = rules.simulate_test_data.output.ref,
-        tgt = rules.simulate_test_data.output.tgt,
-        feature_config = feature_config,
-    output:
-        features = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/{test_seed}/{output_prefix}.features.gz",
-    params:
-        seq_len = seq_len["train"],
-        win_step = win_step,
-        is_phased = lambda wildcards: '--phased' if wildcards.geno_state == 'phased' else '',
-        output_dir = os.path.join(output_dir["test"], "{geno_state}/{test_seed}"),
-        features = "results/data/test/{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/{test_seed}/{output_prefix}.features",
-    log:
-        "logs/process_test_data/{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/{test_seed}/{output_prefix}.log",
-    resources:
-        partition = "himem,gpu",
-        mem_gb = 32,
-        cpus = 16,
-    shell:
-        """
-        gita lr preprocess --vcf {input.vcf} --ref {input.ref} --tgt {input.tgt} --features {input.feature_config} \
-                           --win-len {params.seq_len} --win-step {params.win_step} --output-prefix {wildcards.output_prefix} --output-dir {params.output_dir} \
-                           --worker {resources.cpus} {params.is_phased}
-        gzip -c {params.features} > {output.features} 2> {log}
-        rm {params.features} 2>> {log}
-        """
-
-
-rule test_logistic_regression_model:
-    input:
-        features = rules.process_test_data.output.features,
-        model_file = rules.train_logistic_regression_model.output.model_file,
-    output:
-        pred = "results/performance/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.lr.pred.gz",
-    params:
-        pred = "results/performance/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.lr.pred",
-        output_dir = "results/performance/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}",
-    log:
-        "logs/test_logistic_regression_model/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.log",
-    resources:
-        partition = "himem,gpu",
-        mem_gb = 100,
-    shell:
-        """
-        gita lr infer --features {input.features} --model-file {input.model_file} --output-prefix {output_prefix} --output-dir {params.output_dir}
-        gzip -c {params.pred} > {output.pred} 2> {log}
-        rm {params.pred} 2>> {log}
-        """
-
-
-rule evaluate_logistic_regression_model:
-    input:
-        pred = rules.test_logistic_regression_model.output.pred,
-        true_tracts = lambda wildcards: rules.get_phased_true_tracts.output.bed if wildcards.geno_state == 'phased' else rules.get_unphased_true_tracts.output.bed,
-    output:
-        inferred_tracts = "results/performance/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.lr.{cutoff}.inferred.tracts.bed",
-        performance = "results/performance/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.lr.{cutoff}.performance",
-        summary = "results/performance/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.lr.{cutoff}.performance.summary",
-    params:
-        feature_id = feature_id,
-    log:
-        "logs/evaluate_logistic_regression_model/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.{cutoff}.log",
-    resources:
-        partition = "himem,gpu",
-    shell:
-        """
-        zcat {input.pred} | sed '1d' | awk '$NF>{wildcards.cutoff}' | awk 'BEGIN{{OFS="\\t"}}{{print $1,$2,$3,$4}}' > {output.inferred_tracts} 2>> {log}
-        gita eval --true-tracts {input.true_tracts} --inferred-tracts {output.inferred_tracts} --output {output.performance} 2>> {log}
-        grep -w Summary {output.performance} | awk -v train_demog={wildcards.train_demog} -v test_demog={wildcards.test_demog} \
-                                                  -v geno_state={wildcards.geno_state} -v nref={wildcards.nref} -v ntgt={wildcards.ntgt} \
-                                                  -v train_seed={wildcards.train_seed} -v test_seed={wildcards.test_seed} \
-                                                  -v feature={params.feature_id} -v cutoff={wildcards.cutoff} \
-                                                  'BEGIN{{OFS="\\t"}}{{print train_demog,test_demog,geno_state,nref,ntgt,train_seed,test_seed,feature,cutoff,$2,$3,$4,$5,$6}}' > {output.summary} 2>> {log}
-        """ 
-
-
-rule summary:
-    input:
-        summaries = expand("results/performance/train_{train_demog}_test_{test_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/train_{train_seed}_test_{test_seed}/{output_prefix}.lr.{cutoff}.performance.summary",
-                           train_demog=train_demog, test_demog=test_demog, nref=nref, ntgt=ntgt, geno_state=geno_state_list, output_prefix=output_prefix, train_seed=seed_list["train"], test_seed=seed_list["test"], cutoff=cutoff_list),
-    output:
-        summary = "results/performance/{output_prefix}.performance.summary",
-    log:
-        "logs/summary/{output_prefix}.log",
-    resources:
-        partition = "himem,gpu",
-        mem_gb = 16,
-    shell:
-        """
-        cat {input.summaries} | sed '1iTraining Data Demography\\tTest Data Demography\\tGenotype\\tNref\\tNtgt\\tTraining Seed\\tTest Seed\\tFeature\\tCutoff\\tPrecision\\tRecall\\tTrue_tracts_length\\tInferred_tracts_length\\tOverlaps_length' > {output.summary} 2>> {log}
-        """
diff --git a/workflow/rules/methods/lr/train.gita.lr.smk b/workflow/rules/methods/lr/train.gita.lr.smk
deleted file mode 100644
index 3b120aa..0000000
--- a/workflow/rules/methods/lr/train.gita.lr.smk
+++ /dev/null
@@ -1,49 +0,0 @@
-rule simulate_training_data:
-    input:
-        demes_file = demes["train"],
-        features_config = feature_config,
-    output:
-        features = "results/data/train/{train_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/{train_seed}/{output_prefix}.all.labeled.features",
-    params:
-        nref = nref,
-        ntgt = ntgt,
-        nfeature = nfeature,
-        ref_id = ref_id["train"],
-        tgt_id = tgt_id["train"],
-        src_id = src_id["train"],
-        mut_rate = mut_rate["train"],
-        rec_rate = rec_rate["train"],
-        seq_len = seq_len["train"], 
-        is_phased = lambda wildcards: '--phased' if wildcards.geno_state == 'phased' else '',
-        output_dir = os.path.join(output_dir["train"], "{geno_state}/{train_seed}"),
-    log:
-        "logs/simulate_training_data/{train_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/{train_seed}/{output_prefix}.log",
-    resources:
-        cpus = 16, 
-        mem_gb = 16,
-        time = 120,
-    shell:
-        """
-        gita lr simulate --demes {input.demes_file} --nref {params.nref} --ntgt {params.ntgt} \
-                         --ref-id {params.ref_id} --tgt-id {params.tgt_id} --src-id {params.src_id} \
-                         --mut-rate {params.mut_rate} --rec-rate {params.rec_rate} --seq-len {params.seq_len} \
-                         --output-prefix {wildcards.output_prefix} --output-dir {params.output_dir} \
-                         --seed {wildcards.train_seed} --replicate {resources.cpus} --worker {resources.cpus} \
-                         --feature-config {input.features_config} --nfeature {params.nfeature} {params.is_phased} 2>> {log}
-        """
-
-
-rule train_logistic_regression_model:
-    input:
-        features = rules.simulate_training_data.output.features
-    output:
-        model_file = "results/data/train/{train_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/{train_seed}/{output_prefix}.lr.model",
-    log:
-        "logs/train_logistic_regression_model/{train_demog}/nref_{nref}/ntgt_{ntgt}/{geno_state}/{train_seed}/{output_prefix}.log", 
-    resources:
-        partition = "himem,gpu", 
-        mem_gb = 16,
-    shell:
-        """
-        gita lr train --training-data {input.features} --model-file {output.model_file} --seed {wildcards.train_seed} 2>> {log}
-        """
diff --git a/workflow/rules/methods/unet/test.gita.unet.smk b/workflow/rules/methods/unet/test.gita.unet.smk
deleted file mode 100644
index e69de29..0000000
diff --git a/workflow/rules/methods/unet/train.gita.unet.smk b/workflow/rules/methods/unet/train.gita.unet.smk
deleted file mode 100644
index e69de29..0000000
diff --git a/workflow/rules/methods/unet/apply.gita.unet.smk b/workflow/rules/sai.smk
similarity index 100%
rename from workflow/rules/methods/unet/apply.gita.unet.smk
rename to workflow/rules/sai.smk