In the comments to one of the answers to this question, the asker points out that he is asked to submit his review of a manuscript for publication via email and that there is no formal online system with checkboxes or text boxes. This struck me as strange, as having reviewed papers for several biology and math journals I have never been asked to submit my review via email to the editor. Even for very small journals published independently, I have always been asked to use an online system, where all contact is viewable by the editor-in-chief and other parties at the journal.
Do reputable journals ever ask reviewers to submit their reviews via email, or is such a request a red flag that you are being asked to review for a scam journal? Do all reputable journals have online reviewer systems?
Answer
I have interacted with several reputable math/TCS journals, both as author and as reviewer, entirely via email without the involvement of an online submission. I have even witnessed senior members of the community expressing the sentiment that they never agree to the semi-automated referee requests sent by online submission systems, but only to referee requests sent "by hand".
Summary: Yes, there exist reputable journals conducting peer review entirely by email.
Now whether or not a journal soliciting peer review without an online submission system is more likely to be disreputable than one that does, I do not know. I see no particular reason to assume either way.
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