11

The simplest way of course is to add it to the supplementary materials. However, 220 species are not that many, you should be able to fit that into a page. You have not shown us your tree so it is kind of hard to give specific advice but I am guessing that you have a linear rather than circular tree. If you convert it to a circular tree you should be able to ...


6

To avoid confusion all species names should be written in full at first, and can then be abbreviated. In this particular example it would probably not be a problem to use the second, shorter version. But what if you had four species divided into three genera with all names starting with 'A'? As for question 2, the full name usually only needs to be used in ...


4

Protein-protein interactions is an area of biophysics, so certainly Biophysical Journal (published by Cell) is a nice place to look. PNAS has a broad range of areas and they pay a lot of attention to nice biophysics and modeling. But also they require (seems to me) experimental evidence. The Journal of computational chemistry certainly about a lot of ...


4

This is too long for a comment, so I post it here. And these are my personal views, someone else might handle this different. I would submit the paper to BMC Genomics for some reasons: The editor offered to transfer the paper, so you get past the editorial review. This is not guaranteed for Nature Scientific Report (NSR). You still have to get through the ...


3

When you do science you start with a question or a hypothesis. How is Gene A regulated? Or "does hormone B have an effect on the immune system". Or whatever. Then you start by thinking how you can prove or disprove your question/hypothesis with experiments. You then do your experiments and see if they are enough to prove your question. It often happens that ...


3

Bioinformatics journals can deal perfectly with this type of papers. If you target a journal like Bioinformatics, then you can be as technical as you want (and you probably should). Biologists that read those journals will most likely understand the terminology. Even traditional experimental biology journals, like Nucleic Acids Research, now include a ...


2

Also, don't forget that you can deposit your full tree in treebase. So you can show the collapsed tree in the paper, and give a link to the full tree somewhere in the text.


2

It is not always essential to show a big tree. My opinion might be biased but it seems to me that huge figures with illegible labels are just a gimmick to make the reader feel that it is a great analysis (another case is that of networks). First of all it is important to decide what is that you really want to convey from your figure. For example if your ...


2

It's all about "Is this paper interesting enough to get published?" And people just get a feel for that when they are reading papers all the time, and submitting papers frequently. For instance, maybe publicizing a big cool dataset was useful enough a few years ago to be published as is, but now, you might need a good finding that you found from that ...


1

Journals and services where you can submit your script and manuscript and get DOI: PLOS One F1000 Zenodo CodeOcean


1

Be honest (and possibly split the papers). If the compound was identified as an error and you want to include in a paper describing the process of your simulation and the effectiveness of the predicted inhibitors, you'd have to do so as a sort of negative control for your calculations (unless there is some way to reproduce/rationalise why it showed up ...


1

I disagree somewhat with the others comments. Scientific reports has a broader audience, higher impact factor and is associated with the Nature family of journals. The BMC family of journal family does not have the same reputation and certainly plosONE does not, and has a reputation among some as publishing almost anything. For anyone outside your specific ...


1

I agree with all the responses so far; however I thought I should add that to publish a paper in a decent internationally peer-reviwed journal, more often than not, a paper has to tell a story, ideally a novel story and not just the same data that has been published before or at least address an old question in a new manner, that provides a fresh insight ...


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