diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index f081fe0a8..6f99f7fa0 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -119,7 +119,7 @@ jobs:
           echo "Running cram tests without coverage"
           export AUGUR="${{ github.workspace }}/bin/augur"
         fi
-        cram tests/
+        scripts/run-cram-parallel.py
     - name: Upload coverage
       if: env.COVERAGE_FILE
       uses: actions/upload-artifact@v7
diff --git a/augur/refine.py b/augur/refine.py
index 09479ac77..22fe5ad45 100644
--- a/augur/refine.py
+++ b/augur/refine.py
@@ -5,7 +5,7 @@
 import sys
 from Bio import Phylo
 from textwrap import dedent
-from .argparse_ import ExtendOverwriteDefault
+from .argparse_ import ExtendOverwriteDefault, SKIP_AUTO_DEFAULT_IN_HELP
 from .dates import get_numerical_dates
 from .dates.errors import InvalidYearBounds
 from .io.metadata import DEFAULT_DELIMITERS, DEFAULT_ID_COLUMNS, METADATA_DATE_COLUMN, InvalidDelimiter, Metadata, read_metadata
@@ -174,8 +174,8 @@ def register_parser(parent_subparsers):
                         help="delimiters to accept when reading a metadata file. Only one delimiter will be inferred.")
     parser.add_argument('--metadata-id-columns', default=DEFAULT_ID_COLUMNS, nargs="+", action=ExtendOverwriteDefault,
                         help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.")
-    parser.add_argument('--output-tree', type=str, help='file name to write tree to')
-    parser.add_argument('--output-node-data', type=str, help='file name to write branch lengths as node data')
+    parser.add_argument('--output-tree', type=str, help='file name to write tree to.  If not provided a file will be created using the alignment or tree input path with a "_tt.nwk" suffix.'+SKIP_AUTO_DEFAULT_IN_HELP)
+    parser.add_argument('--output-node-data', type=str, help='file name to write branch lengths as node data. If not provided a file will be created using the alignment or tree input path with a ".node_data.json" suffix.'+SKIP_AUTO_DEFAULT_IN_HELP)
     parser.add_argument('--use-fft', action="store_true", help="produce timetree using FFT for convolutions")
     parser.add_argument('--max-iter', default=2, type=int, help="maximal number of iterations TreeTime uses for timetree inference")
     parser.add_argument('--timetree', action="store_true", help="produce timetree using treetime, requires tree where branch length is in units of average number of nucleotide or protein substitutions per site (and branch lengths do not exceed 4)")
diff --git a/docs/contribute/DEV_DOCS.md b/docs/contribute/DEV_DOCS.md
index 2f6d99ef8..1b1502768 100644
--- a/docs/contribute/DEV_DOCS.md
+++ b/docs/contribute/DEV_DOCS.md
@@ -112,10 +112,18 @@ For example, the following command only runs unit tests related to augur mask.
 ./run_tests.sh -k test_mask
 ```
 
-To run a specific integration test with cram, you can use the following command:
+You can run specific integration test(s) with `cram` directly or via our parallel-wrapper which will use all
+available CPUs by default. For instance to run `tests/functional/clades.t` these will both work:
 
 ```bash
 cram tests/functional/clades.t
+./scripts/run-cram-parallel.py tests/functional/clades.t
+```
+
+To run all tests in parallel simply run
+
+```bash
+./scripts/run-cram-parallel.py
 ```
 
 To run cram tests locally and capture test coverage data, you can use this invocation:
diff --git a/run_tests.sh b/run_tests.sh
index 758b5f226..9dd2850af 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -42,8 +42,8 @@ python3 -m pytest $coverage_arg $filtered_args
 
 # Only run functional tests if we are not running a subset of tests for pytest.
 if [ "$partial_test" = 0 ]; then
-    echo "Running functional tests with cram"
-    cram tests/
+    echo "Running functional tests with cram in parallel via our run-cram-parallel.py runner"
+    ./scripts/run-cram-parallel.py
 else
     echo "Skipping functional tests when running a subset of unit tests"
 fi
diff --git a/scripts/run-cram-parallel.py b/scripts/run-cram-parallel.py
new file mode 100755
index 000000000..f6f999adc
--- /dev/null
+++ b/scripts/run-cram-parallel.py
@@ -0,0 +1,133 @@
+#!/usr/bin/env python3
+"""Run cram tests in parallel using a worker pool."""
+import argparse
+import os
+import subprocess
+import sys
+import time
+from concurrent.futures import ProcessPoolExecutor, as_completed
+from pathlib import Path
+
+# These tests were identified as being particularly slow <https://github.com/nextstrain/augur/issues/1994>
+# We can re-check these over time as we speed up individual tests.
+# We run these tests first to improve parallel efficiency.
+SLOW_TESTS = [
+    "tests/functional/merge/cram/merge-metadata.t",
+    "tests/functional/tree/cram/iqtree-more-threads.t",
+    "tests/functional/subsample/cram/proximal-subsampling.t",
+    "tests/functional/measurements_export.t",
+    "tests/functional/curate/cram/metadata-input.t",
+    "tests/functional/export_v2/cram/metadata-columns.t",
+    "tests/functional/curate/cram/titlecase.t",
+    "tests/functional/tree/cram/iqtree-override-args.t",
+    "tests/functional/subsample/cram/proximal-subsampling-errors.t",
+    "tests/functional/merge/cram/merge-metadata-and-sequences.t",
+]
+
+
+def run_test(test_file, cram_args):
+    start = time.monotonic()
+    result = subprocess.run(
+        ["cram", *cram_args, str(test_file)],
+        capture_output=True,
+    )
+    elapsed = time.monotonic() - start
+    return test_file, result.returncode, elapsed, result.stdout, result.stderr
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description=__doc__,
+        usage="%(prog)s [OPTIONS] [TESTS] [-- CRAM_ARGS...]",
+    )
+    parser.add_argument(
+        "-j", "--jobs", type=int, default=os.cpu_count(),
+        help="number of parallel workers (default: all available (%(default)s))",
+    )
+    parser.add_argument(
+        "tests", nargs="*", default=["tests/"],
+        help="files or directories to find .t files in (default: tests/)",
+    )
+
+    argv = sys.argv[1:]
+    if "--" in argv:
+        split = argv.index("--")
+        args = parser.parse_args(argv[:split])
+        cram_args = argv[split + 1:]
+    else:
+        args = parser.parse_args(argv)
+        cram_args = []
+
+    all_tests = []
+    for path in map(Path, args.tests):
+        if path.is_file():
+            all_tests.append(path)
+        elif path.is_dir():
+            all_tests.extend(path.rglob("*.t"))
+        else:
+            parser.error(f"not a file or directory: {path}")
+    all_tests = sorted(set(all_tests))
+    if not all_tests:
+        parser.error(f"no .t files found in {' '.join(args.tests)}")
+
+    slow_set = [Path(p) for p in SLOW_TESTS]
+    slow_tests = [t for t in slow_set if t in all_tests]
+    rest_tests = [t for t in all_tests if t not in slow_set]
+    test_files = slow_tests + rest_tests
+
+    cram_cmd = " ".join(["cram", *cram_args])
+    print(f"Running {len(test_files)} tests with {args.jobs} workers")
+    print(f"  ({len(slow_tests)} slow tests scheduled first)")
+    print(f"cram invocation: {cram_cmd} <test>\n")
+
+    results = []
+    passed = failed = 0
+    wall_start = time.monotonic()
+
+    with ProcessPoolExecutor(max_workers=args.jobs) as pool:
+        futures = {
+            pool.submit(run_test, t, cram_args): t for t in test_files
+        }
+        for future in as_completed(futures):
+            test_file, rc, elapsed, stdout, stderr = future.result()
+            results.append((elapsed, rc, test_file))
+            status = "PASS" if rc == 0 else "FAIL"
+            if rc == 0:
+                passed += 1
+            else:
+                failed += 1
+            print(f"  {status}  {elapsed:6.1f}s  {test_file}")
+            if rc != 0:
+                if stdout:
+                    print(stdout.decode(errors="replace"))
+                if stderr:
+                    print(stderr.decode(errors="replace"))
+
+    wall_elapsed = time.monotonic() - wall_start
+    total_cpu = sum(e for e, _, _ in results)
+
+    print(f"\n{'='*60}")
+    print(f"Passed: {passed}  Failed: {failed}  Total: {len(results)}")
+    print(f"Wall time:  {wall_elapsed:.1f}s")
+    print(f"Total CPU:  {total_cpu:.1f}s")
+    print(f"Speedup:    {total_cpu / wall_elapsed:.1f}x")
+
+    failures = [(e, rc, t) for e, rc, t in results if rc != 0]
+    if failures:
+        print(f"\n{'='*60}")
+        print(f"Failing tests ({len(failures)}):\n")
+        for elapsed, rc, test_file in sorted(failures, key=lambda x: x[2]):
+            print(f"  {elapsed:6.1f}s  exit={rc}  {test_file}")
+
+    print(f"\n{'='*60}")
+    print("Slowest tests:\n")
+    results.sort(reverse=True)
+    for elapsed, rc, test_file in results[:20]:
+        status = "PASS" if rc == 0 else "FAIL"
+        print(f"  {elapsed:6.1f}s  {status}  {test_file}")
+
+    sys.exit(1 if failures else 0)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tests/functional/refine/cram/keep-ids.t b/tests/functional/refine/cram/keep-ids.t
index 9501db232..16de48aa8 100644
--- a/tests/functional/refine/cram/keep-ids.t
+++ b/tests/functional/refine/cram/keep-ids.t
@@ -9,6 +9,7 @@ Setup
   >  --alignment "$TESTDIR/../data/aligned.fasta" \
   >  --metadata "$TESTDIR/../data/metadata.tsv" \
   >  --output-tree tree.nwk \
+  >  --output-node-data branch_lengths.json \
   >  --timetree \
   >  --clock-filter-iqd 2 \
   >  --seed 314159 2>&1 | grep "pruning leaf" || echo "Nothing pruned"
@@ -28,6 +29,7 @@ Use --keep-ids to force-include it.
   >  --alignment "$TESTDIR/../data/aligned.fasta" \
   >  --metadata "$TESTDIR/../data/metadata.tsv" \
   >  --output-tree tree.nwk \
+  >  --output-node-data branch_lengths.json \
   >  --timetree \
   >  --clock-filter-iqd 2 \
   >  --keep-ids include.txt \
diff --git a/tests/functional/titers/cram/_setup.sh b/tests/functional/titers/cram/_setup.sh
index a19898b77..9c29b1c17 100644
--- a/tests/functional/titers/cram/_setup.sh
+++ b/tests/functional/titers/cram/_setup.sh
@@ -1,3 +1,2 @@
-pushd "$TESTDIR" > /dev/null
-export AUGUR="${AUGUR:-../../../../bin/augur}"
+export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
 set -o pipefail
diff --git a/tests/functional/titers/cram/titers-sub-with-tree-and-custom-prefix.t b/tests/functional/titers/cram/titers-sub-with-tree-and-custom-prefix.t
index a7d095b0a..5c4d1e785 100644
--- a/tests/functional/titers/cram/titers-sub-with-tree-and-custom-prefix.t
+++ b/tests/functional/titers/cram/titers-sub-with-tree-and-custom-prefix.t
@@ -5,13 +5,13 @@ Setup
 Test titer substitution model with alignment and tree inputs and a custom prefix for the node data attributes in the output.
 
   $ ${AUGUR} titers sub \
-  >   --tree ../data/tree.nwk \
-  >   --titers ../data/titers.tsv \
-  >   --alignment ../data/aa_seq_HA1.fasta \
+  >   --tree $TESTDIR/../data/tree.nwk \
+  >   --titers $TESTDIR/../data/titers.tsv \
+  >   --alignment $TESTDIR/../data/aa_seq_HA1.fasta \
   >   --gene-names HA1 \
   >   --attribute-prefix custom_prefix_ \
   >   --output $TMP/titers-sub.json > /dev/null
-  Read titers from ../data/titers.tsv, found:
+  Read titers from */data/titers.tsv, found: (glob)
    --- 62 strains
    --- 15 data sources
    --- 272 total measurements
diff --git a/tests/functional/titers/cram/titers-sub-with-tree.t b/tests/functional/titers/cram/titers-sub-with-tree.t
index 7442f60dc..5a36b2a22 100644
--- a/tests/functional/titers/cram/titers-sub-with-tree.t
+++ b/tests/functional/titers/cram/titers-sub-with-tree.t
@@ -5,12 +5,12 @@ Setup
 Test titer substitution model with alignment and tree inputs.
 
   $ ${AUGUR} titers sub \
-  >   --tree ../data/tree.nwk \
-  >   --titers ../data/titers.tsv \
-  >   --alignment ../data/aa_seq_HA1.fasta \
+  >   --tree $TESTDIR/../data/tree.nwk \
+  >   --titers $TESTDIR/../data/titers.tsv \
+  >   --alignment $TESTDIR/../data/aa_seq_HA1.fasta \
   >   --gene-names HA1 \
   >   --output $TMP/titers-sub.json > /dev/null
-  Read titers from ../data/titers.tsv, found:
+  Read titers from */data/titers.tsv, found: (glob)
    --- 62 strains
    --- 15 data sources
    --- 272 total measurements
diff --git a/tests/functional/titers/cram/titers-tree-with-custom-prefix.t b/tests/functional/titers/cram/titers-tree-with-custom-prefix.t
index e4e221618..3b522c6af 100644
--- a/tests/functional/titers/cram/titers-tree-with-custom-prefix.t
+++ b/tests/functional/titers/cram/titers-tree-with-custom-prefix.t
@@ -5,11 +5,11 @@ Setup
 Test titer tree model with a custom prefix for the node data attributes in the output.
 
   $ ${AUGUR} titers tree \
-  >   --tree ../data/tree.nwk \
-  >   --titers ../data/titers.tsv \
+  >   --tree $TESTDIR/../data/tree.nwk \
+  >   --titers $TESTDIR/../data/titers.tsv \
   >   --attribute-prefix custom_prefix_ \
   >   --output $TMP/titers-tree.json > /dev/null
-  Read titers from ../data/titers.tsv, found:
+  Read titers from */data/titers.tsv, found: (glob)
    --- 62 strains
    --- 15 data sources
    --- 272 total measurements
diff --git a/tests/functional/titers/cram/titers-tree.t b/tests/functional/titers/cram/titers-tree.t
index 5b3bbd4c7..49683b0a0 100644
--- a/tests/functional/titers/cram/titers-tree.t
+++ b/tests/functional/titers/cram/titers-tree.t
@@ -5,10 +5,10 @@ Setup
 Test titer tree model.
 
   $ ${AUGUR} titers tree \
-  >   --tree ../data/tree.nwk \
-  >   --titers ../data/titers.tsv \
+  >   --tree $TESTDIR/../data/tree.nwk \
+  >   --titers $TESTDIR/../data/titers.tsv \
   >   --output $TMP/titers-tree.json > /dev/null
-  Read titers from ../data/titers.tsv, found:
+  Read titers from */data/titers.tsv, found: (glob)
    --- 62 strains
    --- 15 data sources
    --- 272 total measurements
diff --git a/tests/functional/tree/cram/iqtree-compressed-input.t b/tests/functional/tree/cram/iqtree-compressed-input.t
index e82e16d34..b408edee4 100644
--- a/tests/functional/tree/cram/iqtree-compressed-input.t
+++ b/tests/functional/tree/cram/iqtree-compressed-input.t
@@ -4,7 +4,9 @@ Setup
 
 Build a tree with excluded sites using a compressed input file.
 
+  $ cp "$TESTDIR/../data/aligned.fasta.xz" .
+  $ cp "$TESTDIR/../data/excluded_sites.txt" .
   $ ${AUGUR} tree \
-  >  --alignment "$TESTDIR/../data/aligned.fasta.xz" \
-  >  --exclude-sites "$TESTDIR/../data/excluded_sites.txt" \
+  >  --alignment aligned.fasta.xz \
+  >  --exclude-sites excluded_sites.txt \
   >  --output tree_raw.nwk &> /dev/null
diff --git a/tests/functional/tree/cram/iqtree-conflicting-default-args.t b/tests/functional/tree/cram/iqtree-conflicting-default-args.t
index 863e1e1ae..a0968d68c 100644
--- a/tests/functional/tree/cram/iqtree-conflicting-default-args.t
+++ b/tests/functional/tree/cram/iqtree-conflicting-default-args.t
@@ -5,10 +5,11 @@ Setup
 Build a tree with conflicting default arguments.
 Expect error message.
 
+  $ cp "$TESTDIR/../data/aligned.fasta" .
   $ ${AUGUR} tree \
   >  --method iqtree \
-  >  --alignment "$TESTDIR/../data/aligned.fasta" \
-  >  --tree-builder-args="--threads-max 1 --msa $TESTDIR/../data/aligned.fasta" \
+  >  --alignment aligned.fasta \
+  >  --tree-builder-args="--threads-max 1 --msa aligned.fasta" \
   >  --output "tree_raw.nwk"
   ERROR: The following tree builder arguments conflict with hardcoded defaults. Remove these arguments and try again: --threads-max, --msa
   [1]
diff --git a/tests/functional/tree/cram/iqtree-extend-args.t b/tests/functional/tree/cram/iqtree-extend-args.t
index 526ad07b4..99866facf 100644
--- a/tests/functional/tree/cram/iqtree-extend-args.t
+++ b/tests/functional/tree/cram/iqtree-extend-args.t
@@ -4,8 +4,9 @@ Setup
 
 Build a tree, augmenting existing default arguments with custom arguments.
 
+  $ cp "$TESTDIR/../data/aligned.fasta" .
   $ ${AUGUR} tree \
   >  --method iqtree \
-  >  --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --alignment aligned.fasta \
   >  --tree-builder-args="--polytomy" \
   >  --output tree_raw.nwk > /dev/null
diff --git a/tests/functional/tree/cram/iqtree-model-auto.t b/tests/functional/tree/cram/iqtree-model-auto.t
index 5930cce8e..7ef7351a5 100644
--- a/tests/functional/tree/cram/iqtree-model-auto.t
+++ b/tests/functional/tree/cram/iqtree-model-auto.t
@@ -4,8 +4,9 @@ Setup
 
 Try building a tree with IQ-TREE using its ModelTest functionality, by supplying a substitution model of "auto".
 
+  $ cp "$TESTDIR/../data/aligned.fasta" .
   $ ${AUGUR} tree \
-  >  --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --alignment aligned.fasta \
   >  --method iqtree \
   >  --substitution-model auto \
   >  --output tree_raw.nwk \
diff --git a/tests/functional/tree/cram/iqtree-more-threads.t b/tests/functional/tree/cram/iqtree-more-threads.t
index 3b84cf68e..8931d0428 100644
--- a/tests/functional/tree/cram/iqtree-more-threads.t
+++ b/tests/functional/tree/cram/iqtree-more-threads.t
@@ -4,8 +4,9 @@ Setup
 
 Try building a tree with IQ-TREE with more threads (4) than there are input sequences (3).
 
+  $ cp "$TESTDIR/../data/aligned.fasta" .
   $ ${AUGUR} tree \
-  >  --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --alignment aligned.fasta \
   >  --method iqtree \
   >  --output tree_raw.nwk \
   >  --nthreads 4 > /dev/null
diff --git a/tests/functional/tree/cram/iqtree-override-args.t b/tests/functional/tree/cram/iqtree-override-args.t
index 7871e481d..4d3326613 100644
--- a/tests/functional/tree/cram/iqtree-override-args.t
+++ b/tests/functional/tree/cram/iqtree-override-args.t
@@ -5,9 +5,10 @@ Setup
 Build a tree, replacing existing default arguments with custom arguments.
 Since the following custom arguments are incompatible with the default IQ-TREE arguments, this command will only work with the `--override-default-args` flag.
 
+  $ cp "$TESTDIR/../data/full_aligned.fasta" .
   $ ${AUGUR} tree \
   >  --method iqtree \
-  >  --alignment "$TESTDIR/../data/full_aligned.fasta" \
+  >  --alignment full_aligned.fasta \
   >  --tree-builder-args="--polytomy -bb 1000 -bnni" \
   >  --override-default-args \
   >  --output tree_raw.nwk > /dev/null
diff --git a/tests/functional/tree/cram/iqtree-preserve-fa.t b/tests/functional/tree/cram/iqtree-preserve-fa.t
index b1d3ba2f3..3e6e52994 100644
--- a/tests/functional/tree/cram/iqtree-preserve-fa.t
+++ b/tests/functional/tree/cram/iqtree-preserve-fa.t
@@ -4,11 +4,12 @@ Setup
 
 Build a tree with an input file that doesn't end in .fasta, and ensure it's not overwritten.
 
+  $ cp "$TESTDIR/../data/aligned.fa" .
   $ ${AUGUR} tree \
-  >  --alignment "$TESTDIR/../data/aligned.fa" \
+  >  --alignment aligned.fa \
   >  --method iqtree \
   >  --output tree_raw.nwk \
   >  --nthreads 1 > /dev/null
 
-  $ sha256sum "$TESTDIR/../data/aligned.fa" | awk '{print $1}'
+  $ sha256sum aligned.fa | awk '{print $1}'
   169a9f5f70b94e26a2c4ab2b3180d4b463112581438515557a9797adc834863d
diff --git a/tests/functional/tree/cram/iqtree.t b/tests/functional/tree/cram/iqtree.t
index 9b300b06b..1ca945ace 100644
--- a/tests/functional/tree/cram/iqtree.t
+++ b/tests/functional/tree/cram/iqtree.t
@@ -4,8 +4,9 @@ Setup
 
 Try building a tree with IQ-TREE.
 
+  $ cp "$TESTDIR/../data/aligned.fasta" .
   $ ${AUGUR} tree \
-  >  --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --alignment aligned.fasta \
   >  --method iqtree \
   >  --output tree_raw.nwk \
   >  --nthreads 1 > /dev/null