diff --git a/Cargo.lock b/Cargo.lock
index 4bbf24a22b..52c77691c5 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1711,7 +1711,7 @@ dependencies = [
 
 [[package]]
 name = "nextclade"
-version = "3.0.0-alpha.0"
+version = "3.0.0-alpha.1"
 dependencies = [
  "assert2",
  "atty",
@@ -1775,7 +1775,7 @@ dependencies = [
 
 [[package]]
 name = "nextclade-cli"
-version = "3.0.0-alpha.0"
+version = "3.0.0-alpha.1"
 dependencies = [
  "assert2",
  "clap",
@@ -1818,7 +1818,7 @@ dependencies = [
 
 [[package]]
 name = "nextclade-web"
-version = "3.0.0-alpha.0"
+version = "3.0.0-alpha.1"
 dependencies = [
  "assert2",
  "chrono",
diff --git a/packages_rs/nextclade-cli/Cargo.toml b/packages_rs/nextclade-cli/Cargo.toml
index 40b4acc678..85b2d92c73 100644
--- a/packages_rs/nextclade-cli/Cargo.toml
+++ b/packages_rs/nextclade-cli/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "nextclade-cli"
-version = "3.0.0-alpha.0"
+version = "3.0.0-alpha.1"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. CLI module."
 repository = "https://github.com/nextstrain/nextclade"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"
diff --git a/packages_rs/nextclade-web/Cargo.toml b/packages_rs/nextclade-web/Cargo.toml
index 08f8b8da2d..67934c662f 100644
--- a/packages_rs/nextclade-web/Cargo.toml
+++ b/packages_rs/nextclade-web/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "nextclade-web"
-version = "3.0.0-alpha.0"
+version = "3.0.0-alpha.1"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. WebAssembly module."
 edition = "2021"
 license = "MIT"
diff --git a/packages_rs/nextclade/Cargo.toml b/packages_rs/nextclade/Cargo.toml
index e49b356b56..fbeccc8eb8 100644
--- a/packages_rs/nextclade/Cargo.toml
+++ b/packages_rs/nextclade/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "nextclade"
-version = "3.0.0-alpha.0"
+version = "3.0.0-alpha.1"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. Library module."
 repository = "https://github.com/nextstrain/nextclade"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"