The entire guide for authors and referees is available in PDF format.

PRESUBMISSION INQUIRIES
Researchers may request informal feedback from the editors on the journal's interest in a particular manuscript. A short 'presubmission inquiry' can be sent through the online submission system. Researchers should supply a brief paragraph stating the interest to a broad scientific readership, address and contact details, title, a fully referenced summary paragraph, and a list of the references cited in the summary paragraph. Time constraints do not permit editors to read entire manuscripts as presubmission inquiries, and so a reply indicating interest in the work is made on the basis of partial information. Papers that were invited after a presubmission inquiry will occasionally be rejected without review, particularly if the degree of novelty, point of the paper, or existence of overlapping references was not clear.

The presubmission process is designed as a timesaver and to aid in the submission decision for authors. Editors do not enter into extended discussions about these responses. Authors who disagree with a presubmission decision should send in the entire manuscript as a regular submission to our online submission system so that the editors can make a fully informed judgment about whether to review the paper.

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INITIAL SUBMISSION
Papers should be submitted via the online submission system. Each new submission is assigned to a primary editor, who reads the paper, consults with the other editors, and decides whether it should be sent for peer review. Many papers describing solid studies of interest to those in the field are nonetheless judged to be unlikely to compete successfully with the best work submitted to the journal.

Like other journals in the Nature family, Nature Methods has no external editorial board. However, if a paper's importance within the field is unclear, an editor may request advice from outside experts in deciding whether to review it. The novelty of a submitted paper is considered to be compromised if it has significant conceptual overlap with a published paper or one accepted for publication by Nature Methods. Preprint archives do not compromise novelty.

If a paper was previously reviewed at another Nature journal, the authors can use an automated manuscript transfer service to transfer the referees' reports to Nature Methods via a link sent by the editor who handled the manuscript. In that case, the journal editors will take the previous reviews into account when making their decision, although in some cases the editors may choose to take advice from additional or alternative referees. Alternatively, authors may choose to request a fresh review, in which case they should not use the automated transfer link, and the editors will evaluate the paper without reference to the previous review process. However, this decision must be made at the time of initial submission and cannot be changed later. If the authors ask the editors to consider the previous reviews, they should include a note explaining the relationship between the submitted manuscript and the previous submission and (assuming it has been revised in light of the referees' criticisms) giving a point-by-point response to the referees. In cases where the work was felt to be of high quality, papers can sometimes be accepted without further review, but if there were serious criticisms, the editors will consider them in making the decision. In the event of publication, the received date is the date of submission to Nature Methods. More details area available on the manuscript transfer service and on the relationships between Nature titles.

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PEER REVIEW
The corresponding author is notified by e-mail when the editor decides to send a paper for review. Authors may indicate a limited number of scientists who should not review the paper. Excluded scientists must be identified by name. Authors may also suggest referees; these suggestions are often helpful, although they are not always followed. By policy, referees are not identified to the authors or to anyone else outside the journal's editorial office, except at the request of the referee.

Conceptually similar manuscripts are held to the same editorial standards as far as possible, and so they are often sent to the same referees. However, each of the cosubmitted manuscripts must meet the criteria for publication without reference to the other paper. Thus if one paper is substantially less complete or convincing than the other, it may be rejected, even if the papers reach the same conclusion.

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DECISION AFTER REVIEW AND REVISION
When making a decision after review, editors consider not only how good the paper is now, but also how good it might become after revision.

In cases where the referees have requested well-defined changes to the manuscript that do not appear to require extensive further experiments, editors may request a revised manuscript that addresses the referees' concerns. The revised version is normally sent back to some or all of the original referees for re-review. The decision letter will specify a deadline (typically a few weeks), and revisions that are returned within this period will retain their original submission date.

In cases where the referees' concerns are more wide-ranging, editors will normally reject the manuscript. If the editors feel the work is of potential interest to the journal, however, they may express interest in seeing a future resubmission. The resubmitted manuscript may be sent back to the original referees or to new referees, at the editors' discretion. In such cases, revised manuscripts will not retain their earlier submission date.

In either case, the revised manuscript should be accompanied by a cover letter that includes a point-by-point response to referees' comments and an explanation of how the manuscript has been changed.

An invited revision should be submitted via the revision link to the online submission system provided in the decision letter, not as a new manuscript.

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FINAL SUBMISSION AND ACCEPTANCE
A request for final submission is sent when the paper is nearly ready to publish, possibly requiring some text changes but no revisions to the data or conclusions. These letters are accompanied by detailed editorial advice for preparing the final revision. A high priority of Nature Methods is that all papers be accessible to nonspecialists. Manuscripts are subject to substantial editing to achieve this goal. After acceptance, a copy editor may make further changes so that the text and figures are readable and clear to those outside the field, and so that papers conform to our style.

For the final revision, authors should use the revision link to the online submission system provided in the decision letter to upload a final version of the text with all the requested format changes. Electronic files of the final figures, at high resolution, should be sent separately on disk or via ftp.

When all remaining editorial issues are resolved, the paper is formally accepted. The received date is the date on which the editors received the original (or if previously rejected, the resubmitted) manuscript. The accepted date is when the editor sends the acceptance letter.

Contributors are sent proofs and are welcome to discuss proposed changes with the editors, but Nature Methods reserves the right to make the final decision about matters of style and the size of figures.

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APPEALS
Even in cases where editors did not invite resubmission, some authors ask the editors to reconsider a rejection decision. These are considered appeals, which, by policy, must take second place to the normal workload. In practice, this means that decisions on appeals often take several weeks.

Decisions are reversed on appeal only if the editors are convinced that the original decision was a serious mistake, not merely a borderline call that could have gone either way. Further consideration may be merited if a referee made substantial errors of fact or showed evidence of bias, but only if a reversal of that referee's opinion would have changed the original decision. Similarly, disputes on factual issues need not be resolved unless they were critical to the outcome. Thus, after careful consideration of the authors' points, most appeals are rejected by the editors.

If an appeal merits further consideration, the editors may send the authors' response or the revised paper to one or more referees, or they may ask one referee to comment on the concerns raised by another referee. On occasion, particularly if the editors feel that additional technical expertise is needed to make a decision, they may obtain advice from an additional referee.

The entire guide for authors and referees is available in PDF format.

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