From 2f4c623653091e5488db26b61211d553cab6ac45 Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Wed, 6 Sep 2023 15:55:49 +0200
Subject: [PATCH 1/8] fix: return best alignment when band extension hits
 max_band_limit

---
 packages_rs/nextclade/src/align/align.rs      | 33 ++++++++++++-------
 .../nextclade/src/align/seed_alignment.rs     | 11 ++-----
 2 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/packages_rs/nextclade/src/align/align.rs b/packages_rs/nextclade/src/align/align.rs
index 705f295a3..c2b2b849b 100644
--- a/packages_rs/nextclade/src/align/align.rs
+++ b/packages_rs/nextclade/src/align/align.rs
@@ -1,3 +1,5 @@
+use std::cmp::max;
+
 use crate::align::backtrace::{backtrace, AlignmentOutput};
 use crate::align::band_2d::Stripe;
 use crate::align::band_2d::{full_matrix, simple_stripes};
@@ -9,6 +11,7 @@ use crate::alphabet::aa::Aa;
 use crate::alphabet::letter::Letter;
 use crate::alphabet::nuc::Nuc;
 use crate::make_error;
+use bio::alignment;
 use eyre::{Report, WrapErr};
 use log::{info, trace};
 
@@ -62,28 +65,36 @@ pub fn align_nuc(
 
   let mut terminal_bandwidth = params.terminal_bandwidth as isize;
   let mut excess_bandwidth = params.excess_bandwidth as isize;
-  let mut allowed_mismatches = params.allowed_mismatches as isize;
-
+  let mut minimal_bandwidth = max(1, params.allowed_mismatches as isize);
+  let max_band_area = params.max_band_area;
   let mut attempt = 0;
+  let mut alignment: AlignmentOutput<Nuc>;
 
   loop {
-    let stripes = create_alignment_band(
+    let (stripes, band_area) = create_alignment_band(
       &seed_matches,
       qry_len as isize,
       ref_len as isize,
       terminal_bandwidth,
       excess_bandwidth,
-      allowed_mismatches,
-      params.max_band_area,
-    )?;
+      minimal_bandwidth,
+    );
+    if band_area > max_band_area {
+      if attempt == 0 {
+        return make_error!("Alignment matrix size {band_area} exceeds maximum value {max_band_area}. The threshold can be adjusted using CLI flag '--max-band-area' or using 'maxBandArea' field in the dataset's virus_properties.json");
+      }
+      // return previously calculated alignment
+      return Ok(alignment);
+    }
 
-    let mut alignment = align_pairwise(&qry_seq, ref_seq, gap_open_close, params, &stripes);
+    alignment = align_pairwise(&qry_seq, ref_seq, gap_open_close, params, &stripes);
     alignment.is_reverse_complement = is_reverse_complement;
 
-    if alignment.hit_boundary {
-      terminal_bandwidth *= 2;
-      excess_bandwidth *= 2;
-      allowed_mismatches *= 2;
+    if alignment.hit_boundary && minimal_bandwidth > 0 {
+      // double bandwidth parameters or increase to one if 0
+      terminal_bandwidth = max(2 * terminal_bandwidth, 1);
+      excess_bandwidth = max(2 * excess_bandwidth, 1);
+      minimal_bandwidth = max(2 * minimal_bandwidth, 1);
       attempt += 1;
       info!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Band boundary is hit on attempt {}. Retrying with relaxed parameters. Alignment score was: {}", attempt, alignment.alignment_score);
     } else {
diff --git a/packages_rs/nextclade/src/align/seed_alignment.rs b/packages_rs/nextclade/src/align/seed_alignment.rs
index d3877e581..810bd1fe0 100644
--- a/packages_rs/nextclade/src/align/seed_alignment.rs
+++ b/packages_rs/nextclade/src/align/seed_alignment.rs
@@ -215,8 +215,7 @@ pub fn create_alignment_band(
   terminal_bandwidth: isize,
   excess_bandwidth: isize,
   minimal_bandwidth: isize,
-  max_band_area: usize,
-) -> Result<Vec<Stripe>, Report> {
+) -> (Vec<Stripe>, usize) {
   // This function steps through the chained seeds and determines and appropriate band
   // defined via stripes in query coordinates. These bands will later be chopped to reachable ranges
 
@@ -306,13 +305,7 @@ pub fn create_alignment_band(
   // write_stripes_to_file(&stripes, "stripes.csv");
 
   // trim stripes to reachable regions
-  let (regularized_stripes, band_area) = regularize_stripes(stripes, qry_len as usize);
-
-  if band_area > max_band_area {
-    return make_error!("Alignment matrix size {band_area} exceeds maximum value {max_band_area}. The threshold can be adjusted using CLI flag '--max-band-area' or using 'maxBandArea' field in the dataset's virus_properties.json");
-  }
-
-  Ok(regularized_stripes)
+  regularize_stripes(stripes, qry_len as usize)
 }
 
 #[derive(Clone, Copy, Debug)]

From 75d4038efc31bfce429bf63e64bc0eebaaff769f Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Wed, 6 Sep 2023 15:58:12 +0200
Subject: [PATCH 2/8] chore: remove unused import

---
 packages_rs/nextclade/src/align/align.rs | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/packages_rs/nextclade/src/align/align.rs b/packages_rs/nextclade/src/align/align.rs
index c2b2b849b..d470fe084 100644
--- a/packages_rs/nextclade/src/align/align.rs
+++ b/packages_rs/nextclade/src/align/align.rs
@@ -1,5 +1,3 @@
-use std::cmp::max;
-
 use crate::align::backtrace::{backtrace, AlignmentOutput};
 use crate::align::band_2d::Stripe;
 use crate::align::band_2d::{full_matrix, simple_stripes};
@@ -11,9 +9,9 @@ use crate::alphabet::aa::Aa;
 use crate::alphabet::letter::Letter;
 use crate::alphabet::nuc::Nuc;
 use crate::make_error;
-use bio::alignment;
 use eyre::{Report, WrapErr};
 use log::{info, trace};
+use std::cmp::max;
 
 fn align_pairwise<T: Letter<T>>(
   qry_seq: &[T],

From b318dcc0ddde6818a32907850f5e2817ff654873 Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Wed, 6 Sep 2023 17:15:40 +0200
Subject: [PATCH 3/8] chore: remove unused argument in tests

---
 packages_rs/nextclade/src/align/seed_alignment.rs | 2 --
 1 file changed, 2 deletions(-)

diff --git a/packages_rs/nextclade/src/align/seed_alignment.rs b/packages_rs/nextclade/src/align/seed_alignment.rs
index 810bd1fe0..5c8ee9e61 100644
--- a/packages_rs/nextclade/src/align/seed_alignment.rs
+++ b/packages_rs/nextclade/src/align/seed_alignment.rs
@@ -413,7 +413,6 @@ mod tests {
     let max_indel = 100;
     let qry_len = 30;
     let ref_len = 40;
-    let max_band_area = 500_000_000;
 
     let result = create_alignment_band(
       &seed_matches,
@@ -422,7 +421,6 @@ mod tests {
       terminal_bandwidth,
       excess_bandwidth,
       allowed_mismatches,
-      max_band_area,
     );
 
     Ok(())

From 7ef77d736d782ae70e24c688f2fede89fe3e546a Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Wed, 6 Sep 2023 17:25:07 +0200
Subject: [PATCH 4/8] fix: avoid uninitialized alignment

---
 packages_rs/nextclade/src/align/align.rs | 55 ++++++++++++------------
 1 file changed, 27 insertions(+), 28 deletions(-)

diff --git a/packages_rs/nextclade/src/align/align.rs b/packages_rs/nextclade/src/align/align.rs
index d470fe084..5c21a1141 100644
--- a/packages_rs/nextclade/src/align/align.rs
+++ b/packages_rs/nextclade/src/align/align.rs
@@ -66,9 +66,28 @@ pub fn align_nuc(
   let mut minimal_bandwidth = max(1, params.allowed_mismatches as isize);
   let max_band_area = params.max_band_area;
   let mut attempt = 0;
-  let mut alignment: AlignmentOutput<Nuc>;
 
-  loop {
+  let (stripes, band_area) = create_alignment_band(
+    &seed_matches,
+    qry_len as isize,
+    ref_len as isize,
+    terminal_bandwidth,
+    excess_bandwidth,
+    minimal_bandwidth,
+  );
+  if band_area > max_band_area {
+    return make_error!("Alignment matrix size {band_area} exceeds maximum value {max_band_area}. The threshold can be adjusted using CLI flag '--max-band-area' or using 'maxBandArea' field in the dataset's virus_properties.json");
+  }
+
+  let mut alignment = align_pairwise(&qry_seq, ref_seq, gap_open_close, params, &stripes);
+
+  while alignment.hit_boundary && attempt < params.max_alignment_attempts {
+    // double bandwidth parameters or increase to one if 0
+    terminal_bandwidth = max(2 * terminal_bandwidth, 1);
+    excess_bandwidth = max(2 * excess_bandwidth, 1);
+    minimal_bandwidth = max(2 * minimal_bandwidth, 1);
+    attempt += 1;
+    // make new band
     let (stripes, band_area) = create_alignment_band(
       &seed_matches,
       qry_len as isize,
@@ -77,36 +96,16 @@ pub fn align_nuc(
       excess_bandwidth,
       minimal_bandwidth,
     );
+    // discard stripes and break to return previous alignment
     if band_area > max_band_area {
-      if attempt == 0 {
-        return make_error!("Alignment matrix size {band_area} exceeds maximum value {max_band_area}. The threshold can be adjusted using CLI flag '--max-band-area' or using 'maxBandArea' field in the dataset's virus_properties.json");
-      }
-      // return previously calculated alignment
-      return Ok(alignment);
+      break;
     }
-
+    // realign
     alignment = align_pairwise(&qry_seq, ref_seq, gap_open_close, params, &stripes);
-    alignment.is_reverse_complement = is_reverse_complement;
-
-    if alignment.hit_boundary && minimal_bandwidth > 0 {
-      // double bandwidth parameters or increase to one if 0
-      terminal_bandwidth = max(2 * terminal_bandwidth, 1);
-      excess_bandwidth = max(2 * excess_bandwidth, 1);
-      minimal_bandwidth = max(2 * minimal_bandwidth, 1);
-      attempt += 1;
-      info!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Band boundary is hit on attempt {}. Retrying with relaxed parameters. Alignment score was: {}", attempt, alignment.alignment_score);
-    } else {
-      if attempt > 0 {
-        info!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Succeeded without hitting band boundary on attempt {}. Alignment score was: {}", attempt+1, alignment.alignment_score);
-      }
-      return Ok(alignment);
-    }
-
-    if attempt > params.max_alignment_attempts {
-      info!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Attempted to relax band parameters {attempt} times, but still hitting the band boundary. Alignment score was: {}", alignment.alignment_score);
-      return Ok(alignment);
-    }
   }
+
+  alignment.is_reverse_complement = is_reverse_complement;
+  Ok(alignment)
 }
 
 /// align amino acids using a fixed bandwidth banded alignment while penalizing terminal indels

From bd074789f06f1222368fa5ce399ab09d4ce97ef0 Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Wed, 6 Sep 2023 18:06:28 +0200
Subject: [PATCH 5/8] chore: add log messages

---
 packages_rs/nextclade/src/align/align.rs | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/packages_rs/nextclade/src/align/align.rs b/packages_rs/nextclade/src/align/align.rs
index 5c21a1141..fbdc72d07 100644
--- a/packages_rs/nextclade/src/align/align.rs
+++ b/packages_rs/nextclade/src/align/align.rs
@@ -82,6 +82,7 @@ pub fn align_nuc(
   let mut alignment = align_pairwise(&qry_seq, ref_seq, gap_open_close, params, &stripes);
 
   while alignment.hit_boundary && attempt < params.max_alignment_attempts {
+    info!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Band boundary is hit on attempt {}. Retrying with relaxed parameters. Alignment score was: {}", attempt+1, alignment.alignment_score);
     // double bandwidth parameters or increase to one if 0
     terminal_bandwidth = max(2 * terminal_bandwidth, 1);
     excess_bandwidth = max(2 * excess_bandwidth, 1);
@@ -103,7 +104,17 @@ pub fn align_nuc(
     // realign
     alignment = align_pairwise(&qry_seq, ref_seq, gap_open_close, params, &stripes);
   }
-
+  // report success/failure of broadening of band width
+  if alignment.hit_boundary {
+    info!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Attempted to relax band parameters {attempt} times, but still hitting the band boundary. Returning last attempt with score: {}", alignment.alignment_score);
+    if band_area > max_band_area {
+      info!(
+        "When processing sequence #{index} '{seq_name}': final band area {band_area} exceeded the cutoff {max_band_area}"
+      );
+    }
+  } else if attempt > 0 {
+    info!("When processing sequence #{index} '{seq_name}': In nucleotide alignment: Succeeded without hitting band boundary on attempt {}. Alignment score was: {}", attempt+1, alignment.alignment_score);
+  }
   alignment.is_reverse_complement = is_reverse_complement;
   Ok(alignment)
 }

From 867a0e66f99ff5987a3639b4a4bdd478963fac9d Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Thu, 7 Sep 2023 09:40:02 +0200
Subject: [PATCH 6/8] fix: reassign rather than redefine band_area in attempt
 loop to allow reporting after the loop

---
 packages_rs/nextclade/src/align/align.rs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages_rs/nextclade/src/align/align.rs b/packages_rs/nextclade/src/align/align.rs
index fbdc72d07..37e97bfa2 100644
--- a/packages_rs/nextclade/src/align/align.rs
+++ b/packages_rs/nextclade/src/align/align.rs
@@ -67,7 +67,7 @@ pub fn align_nuc(
   let max_band_area = params.max_band_area;
   let mut attempt = 0;
 
-  let (stripes, band_area) = create_alignment_band(
+  let (mut stripes, mut band_area) = create_alignment_band(
     &seed_matches,
     qry_len as isize,
     ref_len as isize,
@@ -89,7 +89,7 @@ pub fn align_nuc(
     minimal_bandwidth = max(2 * minimal_bandwidth, 1);
     attempt += 1;
     // make new band
-    let (stripes, band_area) = create_alignment_band(
+    (stripes, band_area) = create_alignment_band(
       &seed_matches,
       qry_len as isize,
       ref_len as isize,

From 0b2ded4fac07140d3448a16e726c511e68863e05 Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Fri, 8 Sep 2023 07:44:21 +0200
Subject: [PATCH 7/8] refactor(cli): simplify check for completions cli args

---
 packages_rs/nextclade-cli/src/cli/nextclade_cli.rs | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs b/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
index b40772240..bf45763db 100644
--- a/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
+++ b/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
@@ -27,13 +27,6 @@ lazy_static! {
   pub static ref SHELLS: Vec<&'static str> = ["bash", "elvish", "fish", "fig", "powershell", "zsh"].to_vec();
 }
 
-pub fn check_shells(value: &str) -> Result<String, Report> {
-  SHELLS
-    .contains(&value)
-    .then_some(value.to_owned())
-    .ok_or_else(|| eyre!("Unknown shell: '{value}'. Possible values: {}", SHELLS.join(", ")))
-}
-
 #[derive(Parser, Debug)]
 #[clap(name = "nextclade")]
 #[clap(author, version)]
@@ -69,7 +62,7 @@ pub enum NextcladeCommands {
   ///
   Completions {
     /// Name of the shell to generate appropriate completions
-    #[clap(value_name = "SHELL", default_value_t = String::from("bash"), value_parser = check_shells)]
+    #[clap(value_name = "SHELL", default_value_t = String::from("bash"), value_parser = SHELLS.clone())]
     shell: String,
   },
 

From 42fb63fe032c142edcfc3634bea5c0b24d0cbd14 Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Fri, 8 Sep 2023 08:43:22 +0200
Subject: [PATCH 8/8] feat(cli): bring back cli colors using clap v3 styling
 interface

---
 Cargo.lock                                    | 52 +++++++++----------
 packages_rs/nextclade-cli/Cargo.toml          |  6 +--
 .../nextclade-cli/src/cli/nextclade_cli.rs    | 10 ++++
 packages_rs/nextclade/Cargo.toml              |  7 ++-
 4 files changed, 41 insertions(+), 34 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 44d8841e9..b0c6ba611 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -75,16 +75,15 @@ checksum = "4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299"
 
 [[package]]
 name = "anstream"
-version = "0.3.2"
+version = "0.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163"
+checksum = "b1f58811cfac344940f1a400b6e6231ce35171f614f26439e80f8c1465c5cc0c"
 dependencies = [
  "anstyle",
  "anstyle-parse",
  "anstyle-query",
  "anstyle-wincon",
  "colorchoice",
- "is-terminal",
  "utf8parse",
 ]
 
@@ -114,9 +113,9 @@ dependencies = [
 
 [[package]]
 name = "anstyle-wincon"
-version = "1.0.1"
+version = "2.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188"
+checksum = "58f54d10c6dfa51283a066ceab3ec1ab78d13fae00aa49243a45e4571fb79dfd"
 dependencies = [
  "anstyle",
  "windows-sys",
@@ -469,51 +468,42 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.3.10"
+version = "4.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "384e169cc618c613d5e3ca6404dda77a8685a63e08660dcc64abaf7da7cb0c7a"
+checksum = "6a13b88d2c62ff462f88e4a121f17a82c1af05693a2f192b5c38d14de73c19f6"
 dependencies = [
  "clap_builder",
  "clap_derive",
- "once_cell",
-]
-
-[[package]]
-name = "clap-verbosity-flag"
-version = "2.0.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1eef05769009513df2eb1c3b4613e7fad873a14c600ff025b08f250f59fee7de"
-dependencies = [
- "clap",
- "log",
 ]
 
 [[package]]
 name = "clap_builder"
-version = "4.3.10"
+version = "4.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef137bbe35aab78bdb468ccfba75a5f4d8321ae011d34063770780545176af2d"
+checksum = "2bb9faaa7c2ef94b2743a21f5a29e6f0010dff4caa69ac8e9d6cf8b6fa74da08"
 dependencies = [
  "anstream",
  "anstyle",
  "clap_lex",
  "strsim",
+ "unicase",
+ "unicode-width",
 ]
 
 [[package]]
 name = "clap_complete"
-version = "4.3.1"
+version = "4.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f6b5c519bab3ea61843a7923d074b04245624bb84a64a8c150f5deb014e388b"
+checksum = "4110a1e6af615a9e6d0a36f805d5c99099f8bab9b8042f5bc1fa220a4a89e36f"
 dependencies = [
  "clap",
 ]
 
 [[package]]
 name = "clap_complete_fig"
-version = "4.3.1"
+version = "4.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "99fee1d30a51305a6c2ed3fc5709be3c8af626c9c958e04dd9ae94e27bcbce9f"
+checksum = "9e9bae21b3f6eb417ad3054c8b1094aa0542116eba4979b1b271baefbfa6b965"
 dependencies = [
  "clap",
  "clap_complete",
@@ -521,9 +511,9 @@ dependencies = [
 
 [[package]]
 name = "clap_derive"
-version = "4.3.2"
+version = "4.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b8cd2b2a819ad6eec39e8f1d6b53001af1e5469f8c177579cdaeb313115b825f"
+checksum = "0862016ff20d69b84ef8247369fabf5c008a7417002411897d40ee1f4532b873"
 dependencies = [
  "heck",
  "proc-macro2",
@@ -1722,7 +1712,6 @@ dependencies = [
  "bzip2",
  "chrono",
  "clap",
- "clap-verbosity-flag",
  "clap_complete",
  "clap_complete_fig",
  "color-eyre",
@@ -3033,6 +3022,15 @@ version = "1.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "497961ef93d974e23eb6f433eb5fe1b7930b659f06d12dec6fc44a8f554c0bba"
 
+[[package]]
+name = "unicase"
+version = "2.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f7d2d4dafb69621809a81864c9c1b864479e1235c0dd4e199924b9742439ed89"
+dependencies = [
+ "version_check",
+]
+
 [[package]]
 name = "unicode-bidi"
 version = "0.3.13"
diff --git a/packages_rs/nextclade-cli/Cargo.toml b/packages_rs/nextclade-cli/Cargo.toml
index 2b891e126..5d29296b0 100644
--- a/packages_rs/nextclade-cli/Cargo.toml
+++ b/packages_rs/nextclade-cli/Cargo.toml
@@ -11,9 +11,9 @@ publish = false
 
 [dependencies]
 assert2 = "=0.3.11"
-clap = { version = "=4.3.10", features = ["derive"] }
-clap_complete = "=4.3.1"
-clap_complete_fig = "=4.3.1"
+clap = { version = "=4.4.2", features = ["derive", "color", "unicode", "unstable-styles"] }
+clap_complete = "=4.4.1"
+clap_complete_fig = "=4.4.0"
 color-eyre = "=0.6.2"
 comfy-table = "=7.0.1"
 crossbeam = "=0.8.2"
diff --git a/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs b/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
index bf45763db..d732b2e11 100644
--- a/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
+++ b/packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
@@ -3,6 +3,7 @@ use crate::cli::nextclade_dataset_list::nextclade_dataset_list;
 use crate::cli::nextclade_loop::nextclade_run;
 use crate::cli::verbosity::{Verbosity, WarnLevel};
 use crate::io::http_client::ProxyConfig;
+use clap::builder::styling;
 use clap::{ArgGroup, CommandFactory, Parser, Subcommand, ValueEnum, ValueHint};
 use clap_complete::{generate, Generator, Shell};
 use clap_complete_fig::Fig;
@@ -27,10 +28,19 @@ lazy_static! {
   pub static ref SHELLS: Vec<&'static str> = ["bash", "elvish", "fish", "fig", "powershell", "zsh"].to_vec();
 }
 
+fn styles() -> styling::Styles {
+  styling::Styles::styled()
+    .header(styling::AnsiColor::Green.on_default() | styling::Effects::BOLD)
+    .usage(styling::AnsiColor::Green.on_default() | styling::Effects::BOLD)
+    .literal(styling::AnsiColor::Blue.on_default() | styling::Effects::BOLD)
+    .placeholder(styling::AnsiColor::Cyan.on_default())
+}
+
 #[derive(Parser, Debug)]
 #[clap(name = "nextclade")]
 #[clap(author, version)]
 #[clap(verbatim_doc_comment)]
+#[clap(styles = styles())]
 /// Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.
 ///
 /// Nextclade is a part of Nextstrain: https://nextstrain.org
diff --git a/packages_rs/nextclade/Cargo.toml b/packages_rs/nextclade/Cargo.toml
index 3e60a046d..b8b0962d1 100644
--- a/packages_rs/nextclade/Cargo.toml
+++ b/packages_rs/nextclade/Cargo.toml
@@ -18,10 +18,9 @@ auto_ops = "=0.3.0"
 bio = "=1.3.1"
 bio-types = "=1.0.0"
 chrono = { version = "=0.4.26", default-features = false, features = ["clock", "std", "wasmbind"] }
-clap = { version = "=4.3.10", features = ["derive"] }
-clap-verbosity-flag = "=2.0.1"
-clap_complete = "=4.3.1"
-clap_complete_fig = "=4.3.1"
+clap = { version = "=4.4.2", features = ["derive", "color", "unicode", "unstable-styles"] }
+clap_complete = "=4.4.1"
+clap_complete_fig = "=4.4.0"
 color-eyre = "=0.6.2"
 csv = "=1.2.2"
 ctor = "=0.2.2"