diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
index 2318864..70fda3d 100644
--- a/phylogenetic/Snakefile
+++ b/phylogenetic/Snakefile
@@ -18,7 +18,6 @@ rule all:
         auspice_tree = expand("auspice/lassa_{segment}.json", segment=segments)
 
 include: "rules/prepare_sequences.smk"
-include: "rules/prepare_sequences_segments.smk"
 include: "rules/construct_phylogeny.smk"
 include: "rules/annotate_phylogeny.smk"
 include: "rules/export.smk"
diff --git a/phylogenetic/rules/prepare_sequences_segments.smk b/phylogenetic/rules/prepare_sequences_segments.smk
deleted file mode 100644
index 72399d3..0000000
--- a/phylogenetic/rules/prepare_sequences_segments.smk
+++ /dev/null
@@ -1,47 +0,0 @@
-"""
-This part of the workflow prepares sequences for constructing the segment phylogenetic tree.
-
-REQUIRED INPUTS:
-
-    metadata    = data/metadata.tsv
-    sequences   = data/sequences.fasta
-    segment_reference   = defaults/lassa_{segment}.fasta
-
-OUTPUTS:
-
-    metadata    = data/metadata_{segment}.tsv
-    sequences   = data/sequences_{segment}.fasta
-
-This part of the workflow usually includes the following steps:
-
-    - nextclade: Aligns sequences to the reference segment sequence and extracts the segment sequences to ensure the reference files are valid
-    - augur filter: Filters the sequences and metadata to include only the sequences that were successfully aligned
-See Nextclade's usage docs for these commands for more details.
-"""
-
-rule prepare_sequences_segments:
-    input:
-        metadata = "data/metadata.tsv",
-        sequences = "data/sequences.fasta",
-        segment_reference = "defaults/lassa_{segment}.fasta",
-    output:
-        metadata = "data/metadata_{segment}.tsv",
-        sequences = "data/sequences_{segment}.fasta",
-    params:
-        strain_id_field = config["strain_id_field"],
-        min_seed_cover = 0.01,
-    shell:
-        """
-        nextclade run \
-            --input-ref {input.segment_reference} \
-            --output-fasta {output.sequences} \
-            --min-seed-cover {params.min_seed_cover} \
-            --silent \
-            {input.sequences}
-        
-        augur filter \
-            --sequences {output.sequences} \
-            --metadata {input.metadata} \
-            --metadata-id-columns {params.strain_id_field} \
-            --output-metadata {output.metadata}
-        """
\ No newline at end of file