[PRE REVIEW]: `diverse-seq`: an application for alignment-free selecting and clustering biological sequences #7503

editorialbot · 2024-11-19T10:15:05Z

Submitting author: @GavinHuttley (Gavin Huttley)
Repository: https://github.com/HuttleyLab/DiverseSeq
Branch with paper.md (empty if default branch): JOSS
Version: 2024.11.8a3
Editor: @fboehm
Reviewers: @xin-huang, @iimog
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/5069dfd0f172f8d26b43d41b997d0a7c/status.svg)](https://joss.theoj.org/papers/5069dfd0f172f8d26b43d41b997d0a7c)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-11-19T10:15:08Z

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2024-11-19T10:15:26Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1021.2 files/s, 166899.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          27           1060            853           4100
Markdown                        11            226              0            627
Jupyter Notebook                 4              0            464            402
TeX                              3             33              0            232
YAML                             6             48             33            231
TOML                             1             20             17            153
-------------------------------------------------------------------------------
SUM:                            52           1387           1367           5745
-------------------------------------------------------------------------------

Commit count by author:

   346	Gavin Huttley
    77	Robert McArthur
    69	KatherineCaley
     9	dependabot[bot]
     7	GavinHuttley

editorialbot · 2024-11-19T10:15:31Z

Paper file info:

📄 Wordcount for paper.md is 3068

✅ The paper includes a Statement of need section

editorialbot · 2024-11-19T10:15:33Z

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot · 2024-11-19T10:16:30Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: A standardized bacterial taxonomy based on genome ...
- No DOI given, and none found for title: Biometry
- No DOI given, and none found for title: Ensembl 2024
- No DOI given, and none found for title: Numba: a LLVM-based Python JIT compiler
- No DOI given, and none found for title: Robust Locally Weighted Regression and Smoothing S...
- No DOI given, and none found for title: Mash: fast genome and metagenome distance estimati...
- No DOI given, and none found for title: Algorithms for hierarchical clustering: an overvie...
- No DOI given, and none found for title: Some probabilistic and statistical problems on the...

❌ MISSING DOIs

- 10.1109/18.61115 may be a valid DOI for title: Divergence measures based on the Shannon entropy
- 10.1074/mcp.t600022-mcp200 may be a valid DOI for title: DivergentSet, a tool for picking non-redundant seq...
- 10.1038/s41467-019-13443-4 may be a valid DOI for title: Phylogenomics of 10,575 genomes reveals evolutiona...
- 10.1186/gb-2007-8-8-r171 may be a valid DOI for title: PyCogent: a toolkit for making sense from sequence...
- 10.1073/pnas.91.4.1455 may be a valid DOI for title: Reconstructing evolutionary trees from DNA and pro...
- 10.1093/nar/18.20.6097 may be a valid DOI for title: Sequence logos: a new way to display consensus seq...
- 10.1093/molbev/msaa015 may be a valid DOI for title: IQ-TREE 2: new models and efficient methods for ph...
- 10.1038/ismej.2016.168 may be a valid DOI for title: Strategies to improve reference databases for soil...
- 10.1093/oxfordjournals.molbev.a040454 may be a valid DOI for title: The neighbor-joining method: a new method for reco...
- 10.1371/journal.pone.0221068 may be a valid DOI for title: TreeCluster: Clustering biological sequences using...

❌ INVALID DOIs

- None

editorialbot · 2024-11-19T10:16:40Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-11-19T10:17:26Z

Five most similar historical JOSS papers:

VPsearch: fast exact sequence similarity search for genomic sequences
Submitting author: @jvkersch
Handling editor: @lpantano (Active)
Reviewers: @tamarahadz, @sdhutchins
Similarity score: 0.6592

Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments
Submitting author: @marekborowiec
Handling editor: @csoneson (Active)
Reviewers: @iimog, @gavinmdouglas
Similarity score: 0.6577

Mashtree: a rapid comparison of whole genome sequence files
Submitting author: @lskatz
Handling editor: @csoneson (Active)
Reviewers: @luizirber, @standage
Similarity score: 0.6566

SeleDiff: A fast and scalable tool for estimating and testing selection differences between populations
Submitting author: @xin-huang
Handling editor: @lpantano (Active)
Reviewers: @stulacy, @suresh-lab
Similarity score: 0.6335

dms2dfe: Comprehensive Workflow for Analysis of Deep Mutational Scanning Data
Submitting author: @rraadd88
Handling editor: @tracykteal (Retired)
Reviewers: @afrubin
Similarity score: 0.6270

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman · 2025-01-10T08:37:48Z

@GavinHuttley Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Apologies for the delay encountered so far. We have a backlog of submissions to process so we are a bit slower than usual to assign a handling editor. I hope to invite one today.

Before we proceed, please can you have a look at the following points:

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
Lastly, your paper is longer than the usual ~1000 we aim for. If there is any material that is not a JOSS required section that is better suited for your project documentation or as a supplementary document with your project, then please move it there. So please, do some work to reduce the size of your paper. Thanks.

Kevin-Mattheus-Moerman · 2025-01-10T08:40:23Z

@editorialbot invite @fboehm as editor

editorialbot · 2025-01-10T08:40:25Z

Invitation to edit this submission sent!

GavinHuttley · 2025-01-12T22:47:23Z

@editorialbot check references

editorialbot · 2025-01-12T22:47:51Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: A standardized bacterial taxonomy based on genome ...
- No DOI given, and none found for title: Biometry
- No DOI given, and none found for title: Ensembl 2024
- No DOI given, and none found for title: Numba: a LLVM-based Python JIT compiler
- No DOI given, and none found for title: Robust Locally Weighted Regression and Smoothing S...
- No DOI given, and none found for title: Mash: fast genome and metagenome distance estimati...
- No DOI given, and none found for title: Algorithms for hierarchical clustering: an overvie...
- No DOI given, and none found for title: Some probabilistic and statistical problems on the...

❌ MISSING DOIs

- 10.1109/18.61115 may be a valid DOI for title: Divergence measures based on the Shannon entropy
- 10.1074/mcp.t600022-mcp200 may be a valid DOI for title: DivergentSet, a tool for picking non-redundant seq...
- 10.1038/s41467-019-13443-4 may be a valid DOI for title: Phylogenomics of 10,575 genomes reveals evolutiona...
- 10.1186/gb-2007-8-8-r171 may be a valid DOI for title: PyCogent: a toolkit for making sense from sequence...
- 10.1073/pnas.91.4.1455 may be a valid DOI for title: Reconstructing evolutionary trees from DNA and pro...
- 10.1093/nar/18.20.6097 may be a valid DOI for title: Sequence logos: a new way to display consensus seq...
- 10.1093/molbev/msaa015 may be a valid DOI for title: IQ-TREE 2: new models and efficient methods for ph...
- 10.1038/ismej.2016.168 may be a valid DOI for title: Strategies to improve reference databases for soil...
- 10.1093/oxfordjournals.molbev.a040454 may be a valid DOI for title: The neighbor-joining method: a new method for reco...
- 10.1371/journal.pone.0221068 may be a valid DOI for title: TreeCluster: Clustering biological sequences using...

❌ INVALID DOIs

- None

GavinHuttley · 2025-01-12T22:49:39Z

@editorialbot generate pdf

editorialbot · 2025-01-12T22:51:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

GavinHuttley · 2025-01-12T22:51:55Z

@editorialbot check references

editorialbot · 2025-01-12T22:51:59Z

Five most similar historical JOSS papers:

VPsearch: fast exact sequence similarity search for genomic sequences
Submitting author: @jvkersch
Handling editor: @lpantano (Active)
Reviewers: @tamarahadz, @sdhutchins
Similarity score: 0.6591

Mashtree: a rapid comparison of whole genome sequence files
Submitting author: @lskatz
Handling editor: @csoneson (Active)
Reviewers: @luizirber, @standage
Similarity score: 0.6582

Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments
Submitting author: @marekborowiec
Handling editor: @csoneson (Active)
Reviewers: @iimog, @gavinmdouglas
Similarity score: 0.6581

SeleDiff: A fast and scalable tool for estimating and testing selection differences between populations
Submitting author: @xin-huang
Handling editor: @lpantano (Active)
Reviewers: @stulacy, @suresh-lab
Similarity score: 0.6375

dms2dfe: Comprehensive Workflow for Analysis of Deep Mutational Scanning Data
Submitting author: @rraadd88
Handling editor: @tracykteal (Retired)
Reviewers: @afrubin
Similarity score: 0.6294

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

editorialbot · 2025-01-12T22:52:21Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: A standardized bacterial taxonomy based on genome ...
- No DOI given, and none found for title: Biometry
- No DOI given, and none found for title: Ensembl 2024
- No DOI given, and none found for title: Numba: a LLVM-based Python JIT compiler
- No DOI given, and none found for title: Robust Locally Weighted Regression and Smoothing S...
- No DOI given, and none found for title: Mash: fast genome and metagenome distance estimati...
- No DOI given, and none found for title: Algorithms for hierarchical clustering: an overvie...
- No DOI given, and none found for title: Some probabilistic and statistical problems on the...

❌ MISSING DOIs

- 10.1109/18.61115 may be a valid DOI for title: Divergence measures based on the Shannon entropy
- 10.1074/mcp.t600022-mcp200 may be a valid DOI for title: DivergentSet, a tool for picking non-redundant seq...
- 10.1038/s41467-019-13443-4 may be a valid DOI for title: Phylogenomics of 10,575 genomes reveals evolutiona...
- 10.1186/gb-2007-8-8-r171 may be a valid DOI for title: PyCogent: a toolkit for making sense from sequence...
- 10.1073/pnas.91.4.1455 may be a valid DOI for title: Reconstructing evolutionary trees from DNA and pro...
- 10.1093/nar/18.20.6097 may be a valid DOI for title: Sequence logos: a new way to display consensus seq...
- 10.1093/molbev/msaa015 may be a valid DOI for title: IQ-TREE 2: new models and efficient methods for ph...
- 10.1038/ismej.2016.168 may be a valid DOI for title: Strategies to improve reference databases for soil...
- 10.1093/oxfordjournals.molbev.a040454 may be a valid DOI for title: The neighbor-joining method: a new method for reco...
- 10.1371/journal.pone.0221068 may be a valid DOI for title: TreeCluster: Clustering biological sequences using...

❌ INVALID DOIs

- None

GavinHuttley · 2025-01-12T22:53:29Z

@editorialbot commands

editorialbot · 2025-01-12T22:53:33Z

Hello @GavinHuttley, here are the things you can ask me to do:


# List all available commands
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GavinHuttley · 2025-01-12T23:18:19Z

@editorialbot check references

editorialbot · 2025-01-12T23:18:38Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1371/journal.pone.0221068 is OK
- 10.1074/mcp.T600022-MCP200 is OK
- 10.1093/NAR/18.20.6097 is OK
- 10.1109/18.61115 is OK
- 10.1093/nar/gkad1049 is OK
- 10.1038/s41467-019-13443-4 is OK
- 10.1186/gb-2007-8-8-r171 is OK
- 10.1080/01621459.1979.10481038 is OK
- 10.1038/ismej.2016.168 is OK
- 10.1038/nbt.4229 is OK
- 10.1145/2833157.2833162 is OK
- 10.1093/molbev/msaa015 is OK
- 10.1002/widm.53 is OK
- 10.1186/s13059-016-0997-x is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Biometry
- No DOI given, and none found for title: Some probabilistic and statistical problems in the...

❌ MISSING DOIs

- 10.1073/pnas.91.4.1455 may be a valid DOI for title: Reconstructing evolutionary trees from DNA and pro...
- 10.1093/oxfordjournals.molbev.a040454 may be a valid DOI for title: The neighbor-joining method: a new method for reco...

❌ INVALID DOIs

- None

GavinHuttley · 2025-01-23T06:10:09Z

@editorialbot check references

editorialbot · 2025-01-23T06:10:41Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1371/journal.pone.0221068 is OK
- 10.1074/mcp.T600022-MCP200 is OK
- 10.1093/NAR/18.20.6097 is OK
- 10.1109/18.61115 is OK
- 10.1073/pnas.91.4.1455 is OK
- 10.1093/nar/gkad1049 is OK
- 10.1038/s41467-019-13443-4 is OK
- 10.1186/gb-2007-8-8-r171 is OK
- 10.1080/01621459.1979.10481038 is OK
- 10.1093/oxfordjournals.molbev.a040454 is OK
- 10.1038/ismej.2016.168 is OK
- 10.1038/nbt.4229 is OK
- 10.1145/2833157.2833162 is OK
- 10.1093/molbev/msaa015 is OK
- 10.1002/widm.53 is OK
- 10.1186/s13059-016-0997-x is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Biometry
- No DOI given, and none found for title: Some probabilistic and statistical problems in the...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2025-01-23T08:35:57Z

@fboehm can you handle this one?

fboehm · 2025-01-23T14:55:27Z

@editorialbot assign me as editor

editorialbot · 2025-01-23T14:55:31Z

Assigned! @fboehm is now the editor

fboehm · 2025-01-26T01:23:59Z

@jvkersch @lskatz @marekborowiec @xin-huang @rraadd88 - My name is Fred Boehm, and I'm an associate editor for JOSS. Would you be willing to review this submission for JOSS? Please let me know if you have any questions. Thank you!

xin-huang · 2025-01-26T13:36:31Z

Hello @fboehm I can review this paper.

fboehm · 2025-01-27T16:56:54Z

@editorialbot add @xin-huang as reviewer

editorialbot · 2025-01-27T16:56:58Z

@xin-huang added to the reviewers list!

lskatz · 2025-01-27T19:37:58Z

Hi, thank you for including me. Unfortunately, at this time I do not have enough bandwidth.

rraadd88 · 2025-01-27T20:08:42Z

Hi, same here unfortunately at this time. Thanks for the invitation.

fboehm · 2025-01-28T21:10:25Z

@lskatz @rraadd88 - thank you for getting back to me. I hope that we can work together on a future submission.

fboehm · 2025-01-28T21:11:05Z

@luizirber @standage - would you be willing to review this submission for JOSS?

standage · 2025-01-30T13:26:33Z

@fboehm It's unlikely I'll be able to review this until after Feb 14. I will check the status of this submission at that point, and would be happy to review is still needed.

fboehm · 2025-02-06T18:54:15Z

@iimog @gavinmdouglas @tamarahadz @sdhutchins - would you be willing to review this submission for JOSS?

iimog · 2025-02-07T07:56:32Z

Hi @fboehm I'm happy to review this submission.

fboehm · 2025-02-10T16:34:13Z

@editorialbot add @iimog as reviewer

editorialbot · 2025-02-10T16:34:16Z

@iimog added to the reviewers list!

fboehm · 2025-02-10T16:34:35Z

@editorialbot start review

editorialbot · 2025-02-10T16:34:40Z

OK, I've started the review over in #7765.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Nov 19, 2024

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 10, 2025

editorialbot assigned fboehm Jan 23, 2025

editorialbot assigned xin-huang Jan 27, 2025

editorialbot assigned iimog Feb 10, 2025

editorialbot closed this as completed Feb 10, 2025

[PRE REVIEW]: diverse-seq: an application for alignment-free selecting and clustering biological sequences #7503

[PRE REVIEW]: diverse-seq: an application for alignment-free selecting and clustering biological sequences #7503

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lskatz commented Jan 27, 2025

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standage commented Jan 30, 2025

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iimog commented Feb 7, 2025

fboehm commented Feb 10, 2025

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fboehm commented Feb 10, 2025

editorialbot commented Feb 10, 2025

[PRE REVIEW]: `diverse-seq`: an application for alignment-free selecting and clustering biological sequences #7503

[PRE REVIEW]: `diverse-seq`: an application for alignment-free selecting and clustering biological sequences #7503

editorialbot commented Nov 19, 2024 •

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