[PRE REVIEW]: Tree Explorer (T-REX): Bridging Phylogenetic and Phenotypic Data for Enhanced Analysis and Interpretation

[editorialbot]

Submitting author: !--author-handle-->@DamianJM<!--end-author-handle-- (Damian John Magill) Repository: https://github.com/DamianJM/T-REX/ Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (340.5 files/s, 94456.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           1            149            175            812
Markdown                         2             42              0            109
TeX                              1              6              0             70
YAML                             1              1              4             19
-------------------------------------------------------------------------------
SUM:                             5            198            179           1010
-------------------------------------------------------------------------------

Commit count by author:

    15  DamianJM

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 885

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: ETE 3: reconstruction, analysis, and visualization...
- No DOI given, and none found for title: Interactive Tree Of Life (iTOL) v5: an online tool...

❌ MISSING DOIs

- 10.1093/bioinformatics/17.8.754 may be a valid DOI for title: MRBAYES: Bayesian inference of phylogenetic trees
- 10.1038/s41576-020-0233-0 may be a valid DOI for title: Phylogenetic tree building in the genomic age
- 10.1093/molbev/msu300 may be a valid DOI for title: IQ-TREE: a fast and effective stochastic algorithm...
- 10.1093/bioinformatics/btu033 may be a valid DOI for title: RAxML version 8: a tool for phylogenetic analysis ...
- 10.1093/molbev/msab120 may be a valid DOI for title: MEGA11: molecular evolutionary genetics analysis v...

❌ INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

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[Kevin-Mattheus-Moerman]

@DamianJM Dear author, thanks for this submission. I am the AEiC on this track. After reviewing your paper and repository I have come to the conclusion this work is not acceptable for JOSS as it stands. I will therefore proceed to reject this submission.

The following includes some of the reasons for the rejection and other points on the paper/repository, and should be addressed in full if a future re-submission is of interest:

• [ ] Please study the above reference check :point_up: 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/).
• [ ] The project lacks an open source license approved by the Open Source Initiative.
• [ ] Given the small size and limited functionality of the project (<1000 lines of code offering basic GUI interactions and predominantly visualizations), its relative immaturity (single developer, few commits), and poor packaging (single Python file, no license), the project doesn't meet our substantial scholarly effort criterion.

Note that one possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.