diff --git a/docs/images/help.svg b/docs/images/help.svg
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@@ -19,139 +19,139 @@
font-weight: 700;
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- .terminal-3568507036-matrix {
+ .terminal-334567211-matrix {
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@@ -163,46 +163,46 @@
-
+
-
- $ casanovo --help
-
-Usage:casanovo [OPTIONS] COMMAND [ARGS]...
-
- ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
- ┃ Casanovo ┃
- ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
- Casanovo is a state-of-the-art deep learning tool designed for de novo peptide
- sequencing. Powered by a transformer neural network, Casanovo "translates"
- peaks in MS/MS spectra into amino acid sequences.
-
- Links:
-
- • Documentation: https://casanovo.readthedocs.io
- • Official code repository: https://github.com/Noble-Lab/casanovo
-
- If you use Casanovo in your work, please cite:
-
- • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R.,
-Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from
-mass spectra to peptides with a transformer model. in Nature Communications
-15, 6427 (2024). doi:10.1038/s41467-024-49731-x
-
- For more information on how to cite different versions of Casanovo, please see
-https://casanovo.readthedocs.io/en/latest/cite.html.
-
-╭─ Options ────────────────────────────────────────────────────────────────────╮
-│--help-h Show this message and exit. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-╭─ Commands ───────────────────────────────────────────────────────────────────╮
-│configure Generate a Casanovo configuration file to customize. │
-│evaluate Evaluate de novo peptide sequencing performance. │
-│sequence De novo sequence peptides from tandem mass spectra. │
-│train Train a Casanovo model on your own data. │
-│version Get the Casanovo version information │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ casanovo --help
+
+Usage:casanovo [OPTIONS] COMMAND [ARGS]...
+
+ ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
+ ┃ Casanovo ┃
+ ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
+ Casanovo is a state-of-the-art deep learning tool designed for de novo peptide
+ sequencing. Powered by a transformer neural network, Casanovo "translates"
+ peaks in MS/MS spectra into amino acid sequences.
+
+ Links:
+
+ • Documentation: https://casanovo.readthedocs.io
+ • Official code repository: https://github.com/Noble-Lab/casanovo
+
+ If you use Casanovo in your work, please cite:
+
+ • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo
+mass spectrometry peptide sequencing with a transformer model. Proceedings
+of the 39th International Conference on Machine Learning - ICML '22 (2022).
+doi:10.1101/2022.02.07.479481.
+
+ For more information on how to cite different versions of Casanovo, please see
+https://casanovo.readthedocs.io/en/latest/cite.html.
+
+╭─ Options ────────────────────────────────────────────────────────────────────╮
+│--help-h Show this message and exit. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+╭─ Commands ───────────────────────────────────────────────────────────────────╮
+│configure Generate a Casanovo configuration file to customize. │
+│evaluate Evaluate de novo peptide sequencing performance. │
+│sequence De novo sequence peptides from tandem mass spectra. │
+│train Train a Casanovo model on your own data. │
+│version Get the Casanovo version information │
+╰──────────────────────────────────────────────────────────────────────────────╯
+