Frequently asked questions



Frequently asked questions








[under construction]

One of the tools is not working on my computer, how should I proceed ?

Compiling executables that would work on all platforms (e.g., Windows 7, 8, 10 Home, 10 Professional) is a challenge, and we cannot exclude that there might be problems on some platforms. If so, consider using the Python code itself - you will have to install Python and all necessary packages, and then can start the program directly from Python (including the GUI). This will usually be the most stable option and allows to change some settings (e.g., alignment parameters in DNAdiagnoser and TaxI2) that at present cannot be modified from the executables.

I have discovered a real bug in one of the tools, what should I do ?
We recommend you sign up to GitHub, go to the repository of the respective tool, and create a "New Issue" there. The programmer of the respective tool will then correct the bug in the original code. In the next release, also the respective executable will be corrected.

Who may I contact if I have a question ?
So far we do not yet have a dedicated Wiki, discussion group or support email. You can contact one of the lead scientists or developers, but it is recommended for now to submit your questions via GitHub Issues (see previous question).

Why does the webtools link not work ?
Because the webtools are not yet available. To use some of the species delimitation tools online, you can use the Links page to be redirected to web implementations of other labs.

I produce home-made tools or I have innovative ideas of complementary approaches, can I contribute to the next version of iTaxoTools?
Yes, iTaxoTools is first and foremost a collaborative project designed for and by taxonomists, and jointly with various bioinformatics programmers. Any suggestion of new tools answering our philosophy is welcome!

Why, as a taxonomist, should I trust these automated delimitation tool whereas I can see that their results are sometimes very questionable?
The available species delimitation tools are only intended to explore the most likely species partitions within a given dataset and under specific assumptions. They allows taxonomists to infer species boundaries based on different detection criteria, such as barcode gap, coalescence, or monophyly, and will therefore very likely provide disparate results. The results inferred by a given method should therefore be considered with caution, and are to be regarded as an objective decision aid for partitioning individuals into initial species hypothesis that can then be subsequently tested in an integrative taxonomy pipeline, in combination with other datasets and methods.

Your initiative seems to be interesting, but actually it is useless for me (I am only working with morphological data !)
This first release of iTaxoTools is indeed mainly focused on molecular datasets, but new developments will allow to optimize morphological datasets and, if needed, to integrate them to molecular datasets.

Why so many questions ?
Because it is a FAQ webpage..