{"action":"created","issue":{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/593","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/593/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/593/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/593/events","html_url":"https://github.com/openjournals/joss-reviews/issues/593","id":299356935,"number":593,"title":"[REVIEW]: Phylen: automatic phylogenetic reconstruction using the EggNOG database","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars3.githubusercontent.com/u/18508068?v=4","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"id":330465313,"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04","default":false}],"state":"open","locked":false,"assignee":{"login":"Kevin-Mattheus-Moerman","id":8392709,"avatar_url":"https://avatars0.githubusercontent.com/u/8392709?v=4","gravatar_id":"","url":"https://api.github.com/users/Kevin-Mattheus-Moerman","html_url":"https://github.com/Kevin-Mattheus-Moerman","followers_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/followers","following_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/following{/other_user}","gists_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/gists{/gist_id}","starred_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/subscriptions","organizations_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/orgs","repos_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/repos","events_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/events{/privacy}","received_events_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/received_events","type":"User","site_admin":false},"assignees":[{"login":"Kevin-Mattheus-Moerman","id":8392709,"avatar_url":"https://avatars0.githubusercontent.com/u/8392709?v=4","gravatar_id":"","url":"https://api.github.com/users/Kevin-Mattheus-Moerman","html_url":"https://github.com/Kevin-Mattheus-Moerman","followers_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/followers","following_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/following{/other_user}","gists_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/gists{/gist_id}","starred_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/subscriptions","organizations_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/orgs","repos_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/repos","events_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/events{/privacy}","received_events_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/received_events","type":"User","site_admin":false}],"milestone":null,"comments":14,"created_at":"2018-02-22T13:37:52Z","updated_at":"2018-02-22T20:34:35Z","closed_at":null,"author_association":"COLLABORATOR","body":"**Submitting author:** @giraola (<a href=\"http://orcid.org/0000-0002-6516-3404\">Gregorio Iraola</a>)\r\n**Repository:** <a href=\"https://github.com/iferres/phylen\" target =\"_blank\">https://github.com/iferres/phylen</a>\r\n**Version:** v0.1.0\r\n**Editor:** @Kevin-Mattheus-Moerman\r\n**Reviewer:** @juanvillada\r\n**Archive:** Pending\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/aeedb5e6a0e6d0cd88ec273eb50e1254/status.svg)](http://joss.theoj.org/papers/aeedb5e6a0e6d0cd88ec273eb50e1254)\r\n\r\nStatus badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/aeedb5e6a0e6d0cd88ec273eb50e1254\"><img src=\"http://joss.theoj.org/papers/aeedb5e6a0e6d0cd88ec273eb50e1254/status.svg\"></a>\r\nMarkdown: [![status](http://joss.theoj.org/papers/aeedb5e6a0e6d0cd88ec273eb50e1254/status.svg)](http://joss.theoj.org/papers/aeedb5e6a0e6d0cd88ec273eb50e1254)\r\n```\r\n**Reviewers and authors**:\r\n\r\nPlease avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the <a href=\"https://github.com/iferres/phylen\" target=\"_blank\">target repository</a> and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)\r\n\r\n## Reviewer instructions & questions\r\n---\r\n**REVIEWER 1**   \r\n\r\n@juanvillada, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:\r\n1. Make sure you're logged in to your GitHub account\r\n2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations\r\n\r\nThe reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.\r\n\r\n  ### Conflict of interest\r\n\r\n- [ ] As the reviewer I confirm that I have read the [JOSS conflict of interest policy](https://github.com/openjournals/joss/blob/master/COI.md) and that there are no conflicts of interest for me to review this work.\r\n\r\n### Code of Conduct\r\n\r\n- [ ] I confirm that I read and will adhere to the [JOSS code of conduct](https://joss.theoj.org/about#code_of_conduct).\r\n\r\n### General checks\r\n\r\n- [ ] **Repository:** Is the source code for this software available at the <a target=\"_blank\" href=\"https://github.com/iferres/phylen\">repository url</a>?\r\n- [ ] **License:** Does the repository contain a plain-text LICENSE file with the contents of an [OSI approved](https://opensource.org/licenses/alphabetical) software license?\r\n- [ ] **Version:** Does the release version given match the GitHub release (v0.1.0)?\r\n- [ ] **Authorship:** Has the submitting author (@giraola) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?\r\n\r\n### Functionality\r\n\r\n- [ ] **Installation:** Does installation proceed as outlined in the documentation?\r\n- [ ] **Functionality:** Have the functional claims of the software been confirmed?\r\n- [ ] **Performance:** If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)\r\n\r\n### Documentation\r\n\r\n- [ ] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **Installation instructions:** Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.\r\n- [ ] **Example usage:** Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality documentation:** Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?\r\n- [ ] **Automated tests:** Are there automated tests or manual steps described so that the function of the software can be verified?\r\n- [ ] **Community guidelines:** Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\n- [ ] **Authors:** Does the `paper.md` file include a list of authors with their affiliations?\r\n- [ ] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **References:** Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?\r\n\r\n---\r\n**REVIEWER 2**   \r\n\r\n@kortschak, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:\r\n1. Make sure you're logged in to your GitHub account\r\n2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations\r\n\r\nThe reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.\r\n\r\n  ### Conflict of interest\r\n\r\n- [ ] As the reviewer I confirm that I have read the [JOSS conflict of interest policy](https://github.com/openjournals/joss/blob/master/COI.md) and that there are no conflicts of interest for me to review this work.\r\n\r\n### Code of Conduct\r\n\r\n- [ ] I confirm that I read and will adhere to the [JOSS code of conduct](https://joss.theoj.org/about#code_of_conduct).\r\n\r\n### General checks\r\n\r\n- [ ] **Repository:** Is the source code for this software available at the <a target=\"_blank\" href=\"https://github.com/iferres/phylen\">repository url</a>?\r\n- [ ] **License:** Does the repository contain a plain-text LICENSE file with the contents of an [OSI approved](https://opensource.org/licenses/alphabetical) software license?\r\n- [ ] **Version:** Does the release version given match the GitHub release (v0.1.0)?\r\n- [ ] **Authorship:** Has the submitting author (@giraola) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?\r\n\r\n### Functionality\r\n\r\n- [ ] **Installation:** Does installation proceed as outlined in the documentation?\r\n- [ ] **Functionality:** Have the functional claims of the software been confirmed?\r\n- [ ] **Performance:** If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)\r\n\r\n### Documentation\r\n\r\n- [ ] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **Installation instructions:** Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.\r\n- [ ] **Example usage:** Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality documentation:** Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?\r\n- [ ] **Automated tests:** Are there automated tests or manual steps described so that the function of the software can be verified?\r\n- [ ] **Community guidelines:** Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\n- [ ] **Authors:** Does the `paper.md` file include a list of authors with their affiliations?\r\n- [ ] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **References:** Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?\r\n\r\n---\r\n**REVIEWER 3**   \r\n\r\n@KlausVigo, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:\r\n1. Make sure you're logged in to your GitHub account\r\n2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations\r\n\r\nThe reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.\r\n\r\n  ### Conflict of interest\r\n\r\n- [ ] As the reviewer I confirm that I have read the [JOSS conflict of interest policy](https://github.com/openjournals/joss/blob/master/COI.md) and that there are no conflicts of interest for me to review this work.\r\n\r\n### Code of Conduct\r\n\r\n- [ ] I confirm that I read and will adhere to the [JOSS code of conduct](https://joss.theoj.org/about#code_of_conduct).\r\n\r\n### General checks\r\n\r\n- [ ] **Repository:** Is the source code for this software available at the <a target=\"_blank\" href=\"https://github.com/iferres/phylen\">repository url</a>?\r\n- [ ] **License:** Does the repository contain a plain-text LICENSE file with the contents of an [OSI approved](https://opensource.org/licenses/alphabetical) software license?\r\n- [ ] **Version:** Does the release version given match the GitHub release (v0.1.0)?\r\n- [ ] **Authorship:** Has the submitting author (@giraola) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?\r\n\r\n### Functionality\r\n\r\n- [ ] **Installation:** Does installation proceed as outlined in the documentation?\r\n- [ ] **Functionality:** Have the functional claims of the software been confirmed?\r\n- [ ] **Performance:** If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)\r\n\r\n### Documentation\r\n\r\n- [ ] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **Installation instructions:** Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.\r\n- [ ] **Example usage:** Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality documentation:** Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?\r\n- [ ] **Automated tests:** Are there automated tests or manual steps described so that the function of the software can be verified?\r\n- [ ] **Community guidelines:** Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\n- [ ] **Authors:** Does the `paper.md` file include a list of authors with their affiliations?\r\n- [ ] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **References:** Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?\r\n"},"comment":{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/comments/367813343","html_url":"https://github.com/openjournals/joss-reviews/issues/593#issuecomment-367813343","issue_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/593","id":367813343,"user":{"login":"Kevin-Mattheus-Moerman","id":8392709,"avatar_url":"https://avatars0.githubusercontent.com/u/8392709?v=4","gravatar_id":"","url":"https://api.github.com/users/Kevin-Mattheus-Moerman","html_url":"https://github.com/Kevin-Mattheus-Moerman","followers_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/followers","following_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/following{/other_user}","gists_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/gists{/gist_id}","starred_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/subscriptions","organizations_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/orgs","repos_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/repos","events_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/events{/privacy}","received_events_url":"https://api.github.com/users/Kevin-Mattheus-Moerman/received_events","type":"User","site_admin":false},"created_at":"2018-02-22T20:34:35Z","updated_at":"2018-02-22T20:34:35Z","author_association":"COLLABORATOR","body":"@juanvillada (reviewer 1) @kortschak (reviewer 2) @KlausVigo (reviewer 3) we are good to go for the review process. Let me know if you are not able to tick the boxes at the top of this issue (be sure to accept this invite: https://github.com/openjournals/joss-reviews/invitations). \r\nIf you have questions just ping me or check out the [reviewer guidelines](http://joss.theoj.org/about#reviewer_guidelines). THANKS! :tada: "}}
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