diff --git a/tools/nextclade/macros.xml b/tools/nextclade/macros.xml
index b18577d940e..2c9b2034576 100644
--- a/tools/nextclade/macros.xml
+++ b/tools/nextclade/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools -->
-    <token name="@TOOL_VERSION@">3.5.0</token>
+    <token name="@TOOL_VERSION@">3.6.0</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">@online{nextclade,