I have done extensive research on trying to find free software that I can use to create publication quality structure diagrams with but have yet to find something suitable.

Tools I currently know about are:

  • Xmind
  • Freeplane
  • FreeMind

And then there are a bunch listed here.

The problem with all of these are that they either make mind-maps that have quirky stiles that don't look very technical/professional or they don't support PDF or PS or high quality bitmap exporting.

I really like XMind, but the free version export totally rubish quality bitmaps and no PDF.

I currently use Libreoffice Draw, but I have to manually place objects and manually connect them with lines and arrows etc. Thus not a very efficient workflow.

To clarify my need:

I am doing engineering research so I am in look of something more utilitarian than 'pretty', although I like for the figures I create to be soft on the eyes as well. To sumarize, efficiency of use and clarity of the structure diagram are the important factors.

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    I’m voting to close this question as off-topic because there is no discernible relation to Academia. It may be on-topic on Software Recommendations. – Wrzlprmft Sep 4 '15 at 8:50
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    Also note that mind maps are a very specific thing with strong restrictions (and rather silly in my opinion). What you probably want are structure diagrams, flow charts and similar. Do not devaluate the latter by calling them mind maps. – Wrzlprmft Sep 4 '15 at 8:55
  • Firstly, I didn't know about that group. Secondly, I don't really agree with you that it's not relevant to academics. Journals require high quality figures for publication and I am sure most seasoned academics have a way to produce high quality mind-maps, no matter what their field of research. An OK, I will call them structure diagrams yes. Rather than immediately shoot down my question, do you perhaps have a tool you can recomend @Wrzlprmft? Thanks! – Jonny Sep 4 '15 at 8:56
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    The key word is discernible. Clarify what specific academic needs you have and I will happily retract my close vote and perhaps answer. – Wrzlprmft Sep 4 '15 at 9:03
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    Also, Dia ia a free choice (for flow charts). And a paid tool is Visio. – Alexandros Sep 4 '15 at 9:19

yEd can produce the 'research grade' diagrams that you'd be interested in.

  • It can produce nearly all sorts of figures includeing graphs, network diagrams, flow charts, architecture diagrams and block diagrams.
  • It has a whole wide range of auto arrange feature to rearrange your blocks creating a great professional look for a structure diagram.
  • It can export diagrams in vetor graphics, which includes PDF, PS, EPS, SVG and so on.
  • It produces graphml as save file making it cross compatible with graphml coders
  • Most importantly, it is cross-platform compatable, be it Mac, Windows or Linux.
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  • Wow thanks Ebe, yEd looks really like exactly what I was looking for. especially applicable since I work between Windows and Linux. – Jonny Sep 4 '15 at 10:14

If you want a lot of control over how your diagram is looking and are not afraid to put in a little bit of work you can also use inkscape. This caters more to your 'clarity of structures' needs than ease of use and would require some time to learn. In my opinion this is time well spent though.

Inkscape is a vector graphics program, so you would have to create each node by yourself. It might handle a little like LibreOffice Draw, but offers a lot more functionality. Here is a link with some tips how to create nice diagrams in inkscape. The newest version of inkscape also has a diagram connector tool which take off some of the work though. Additionally inkscape offers a really good (manual) alignment tool to place your nodes.

Inkscape creates svg files but supports export to pdf and high resolution png files.

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First of all, I suggest you to update your question's title by replacing 'best' with some more appropriate word. The reason is rather simple: IMHO, whenever one is asking about something, using terms 'best' or similar, he/she should specify corresponding criteria, since potential answers might/will be very different, depending on those criteria. In the lack of specifying criteria, such question doesn't make much sense and, thus, cannot be answered. Secondly, questions, asking to recommend software with a comparison twist, usually strongly imply people's opinions. Such questions typically are frowned upon on StackExchange, in general, and on this site, in particular (though, there are numerous exclusions from that "standard" approach, which often makes thongs quite confusing). Thirdly, software that you mentioned in your question belongs to the class of mind-mapping software, which is quite different from general diagramming software. All the above-mentioned points are not to criticize you, but to establish some context for the rest of my answer.

While previous comments and answers mentioned some good general diagramming tools, such as Dia, yEd and GraphViz, I am very surprised that neither you are aware of, nor anybody has advised such extremely popular tools for publications, especially in the engineering context, as LaTeX and various relevant LaTeX packages. I highly recommend you to take a look at such packages, as tikz (pretty much, the gold standard for LaTeX diagramming), mindmap and smartdiagram. They, as most things, related to LaTeX, have rather high learning curve (especially tikz), but for many people and applications the time and effort spent are well worth it. In order to support and illustrate my recommendations, feel free to take a look at my Ph.D. dissertation defense presentation slides, which I have prepared with the help of all packages, mentioned above (and then some). For the general LaTeX-based diagrams, please see slides 15, 16, 17, 21, 23, 25, 27, 35, 40, 44 and 51.

A couple of examples from the presentation (for those not wanting to leave this site):

enter image description here

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Final note: in many situations, especially in research and engineering context, a very significant benefit of using LaTeX-based approach is the ability of automating diagrams and other resulting artifacts generation. This aspect is IMHO very important from the reproducibility perspective.

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    For more ideas about what can be done with TikZ, check out this website. – Aleksandr Blekh Sep 4 '15 at 11:17
  • Thanks Aleksandr, I did rephrase the title of my question slightly. I do actually use Latex for all my writing and my writing of my master's thesis, but have never played around with any 'graphics' related packages. I will check it out! – Jonny Sep 4 '15 at 12:28
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    @Jonny: You are welcome. Glad to hear that you use LaTeX. In terms of its visualization packages, I am pretty sure that you will be pleasantly surprised. – Aleksandr Blekh Sep 4 '15 at 22:12

I'm fond of Graphviz, which can generate all sorts of diagrams, with high-quality output. One of the advantages of Graphviz is that the input format is simple and natural. This in turn makes it easy to write scripts that automatically generate diagrams based on your latest data.

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