Clade I example sequences

nextstrain · Aug 8, 2024 · 5e52962 · 5e52962
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diff --git a/nextclade/resources/clade-i/README.md b/nextclade/resources/clade-i/README.md
@@ -21,7 +21,7 @@ The reference used in this dataset is [DQ011155.1](https://www.ncbi.nlm.nih.gov/
 
 This is in contrast to the reference used in the other Nextclade mpox datasets, which use a clade IIb reference sequence.
 
-The reference tree consists of all good quality clade I sequences available within Genbank at the time of dataset creation, as well as 3 outgroup genomes (a reconstructed ancestor of all clades, and one sequence for each of clade IIa and clade IIb).
+The reference tree consists of all good quality clade I sequences available within Genbank at the time of dataset creation (with identical sequences deduplicated to 1), as well as 3 outgroup genomes (a reconstructed ancestor of all clades, and one sequence for each of clade IIa and clade IIb).
 
 ## Further reading
 

diff --git a/nextclade/resources/clade-i/auspice_config_patch.json b/nextclade/resources/clade-i/auspice_config_patch.json
@@ -3,5 +3,59 @@
     "op": "replace",
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 ]
diff --git a/nextclade/resources/clade-i/pathogen.json b/nextclade/resources/clade-i/pathogen.json
@@ -1,16 +1,16 @@
 {
   "alignmentParams": {
-    "allowedMismatches": 5,
-    "excessBandwidth": 40,
-    "gapAlignmentSide": "left",
+    "excessBandwidth": 100,
+    "terminalBandwidth": 300,
+    "allowedMismatches": 8,
+    "windowSize": 40,
     "minSeedCover": 0.1,
-    "terminalBandwidth": 200,
-    "windowSize": 30
+    "gapAlignmentSide": "left"
   },
   "attributes": {
     "name": "Mpox virus (Clade I)",
-    "reference accession": "NC_063383.1",
-    "reference name": "MPXV-M5312_HM12_Rivers"
+    "reference accession": "DQ011155.1",
+    "reference name": "Zaire_1979-005"
   },
   "compatibility": {
     "cli": "3.0.0-alpha.0",