When you posted your first review, I had just started working for Biomatters. Also, I agreed more with your first review than with your second one, so I didn’t feel as much need to comment on it and provide my point of view.

> My first “positive” review praised the first version of Geneious. My
> second “negative” one “slammed” it, or maybe just gave a little bit of
> balance to the initial review. I agree that the number of free features in
> Geneious is good and software is always limiting. But with no bias,
> compare the pro and free versions.

I still think that you are making an unfair comparison here. So there is another program (called Geneious Pro) that is better than Geneious, but costs money. How does this make the free program any worse? I understand that you would be more happy if Geneious Pro was free too, and open source and everything. Who wouldn’t like that? The problem is that if Geneious Pro was open source, it wouldn’t exist, because there wouldn’t have been sufficient interest in creating it. So I think the only two realistic options are a) a world with free Geneious and commercial Geneious Pro against b) a world with no Geneious at all. Which is better?

I regard Biomatters as the prime example of a company that doesn’t have purely commercial goals. Yes, we want to earn enough money to survive (and keep doing what we do), how is that a bad thing? If we didn’t, we would be bankrupt today (like the bioOpen guys, which is a pity for the whole scientific community) and there would be no Geneious, not even the free version. As we are not funded by the state as many universities are, we have to earn our money from our users – and I think we are giving them a very good deal, i.e. most of our users probably increase their income by a lot more than what they spent on the Pro license, and many others have never bought any Pro license, but still speed up their research using Geneious, which is also great software.

> Regarding the interface, you can find similar or even better features in
> BioEdit, which is also free. But it has major disadvantages, as being
> Windows-only and being focused only on sequence alignment. Other software
> that can be comparable to Geneious is bioOpen, but falls in the same
> category as BioEdit: Mac-only and not even free. I don’t know the price of
> bioOpen but its ordering form gives you the option to select which
> functionalities you want.

You have given the caveats yourself, and now we have to add that BioOpen is bankrupt. I think this only supports my point that Geneious (+Pro) is good for the community, and it is in the community members’ own interest to support us in return.

> I was never a bioinformatics student, maybe because during my time there
> were not many bioinformatics courses available, even more where I did my
> graduate studies. So I cannot give you a personal view as a
> “bioinformatics student”. But first, we have to separate bioinformatics
> students in two classes (too few maybe): the computer scientist that
> understands biology and the biologist that programs computers. You can
> even include here a third class which is the computer-savvy biologist:
> he/she cannot program but have a high knowledge of computers.
>
> With our categories defined I ask you again: what are the benefits of
> writing a plug-in for Geneious for each one of these classes of users?

I don’t see why the reason would be different for the different classes. If they can’t program at all, they don’t need a reason because they can’t write a custom program either with Geneious nor from scratch. And if they know enough about programming to be able to hack together a program, then they can instead also do it a lot easier (because they don’t have to do the GUI and the file import/export) as a plugin for Geneious. The latter also makes it a lot easier to use their tool in combination with others, and it makes it a lot more likely that the tool will be of use on a different platform (Windows/MacOS/Linux) and in 10 years, to anyone who uses Geneious – which is free.

> If I am a bench biologist with zero knowledge of programming do I have to
> wait for someone write me a plug-in or wait for Biomatters to include in
> Geneious?

Yes, or you can hire someone to do it for you. If Geneious didn’t exist,
then you wouldn’t even have those options. You would be restricted to
using the other alternatives (such as BioJava), and there’s a good chance
that this would be harder than writing a plugin for Geneious.

> Of course it makes a program more usable for a lot more people. People
> that are using Geneious, right? How do you measure peer respect? By doing
> a wonderful program from scratch or by adding to a proprietary software a
> plug-in? Or, wouldn’t be better to create a open source project (or join
> one) that works in bioinformatics development?

Empirical point: Look around you. How many open source projects exist that
offer the same functionality as Geneious Pro for free? Zero. Nada. None.
You’re comparing something that exists with something for which there isn’t
enough incentive for it to exist in today’s environment. I would also
prefer if I could get my car for free, a house too, and did I mention I’d
like to go on a date with Jennifer Anniston? All this would be nice, but
it won’t happen, so I’m doing the best with my life that is actually
possible.

By the way, there’s no reason why you can’t publish your Geneious plugin
as open source.

> I did my Masters writing software and my PhD working on phylogenetics.
> Would Geneious help me in the first case? No (maybe with ideas). Would it
> help me in the latter? Definitely, yes. Would I spend time during my PhD
> to write plug-ins to Geneious? No. See the difference?

And for what reasons would you choose not to write your software as a
plugin? See my reasons above why it is in our own interest to *do* write your software in the form of a Geneious plugin.

> There were only two at the time of my review. It is good that it is
> increasing, 100% in a couple of days. And going back to the “peer
> respect”, I downloaded MrBayes plug-in and I couldn’t find the names of
> the developers. Also could not find any reference to MrBayes authors,
> papers, etc.

As Richard pointed out, the authors of each plugin are credited inside Geneious. But I agree they should be listed on the plugin download page too. We will restructure that page after the 3.0 release, to make sure that references are sufficiently visible.

Cheers,

Tobias