MicrobeTrace and its Alternatives
MicrobeTrace is a tool that's trying to make a particular type of analysis easier. There are some other, similar tools trying to accomplish the same thing. Let's talk about a few of them, and compare pros and cons:
HIV-TRACE, or HIV-TRAnsmission Clustering Engine is a software package designed to consume a FASTA file containing HIV sequences, compute a genetic distance matrix (using the tn93 algorithm), label pairwise links between sequences according to whether they fall below a predefined threshold, and output the results.
If this sounds vaguely familiar, that's because it's almost exactly what MicrobeTrace does. And there's a good reason for this: MicrobeTrace was originally a wrapper for HIV-TRACE. However, circa Spring of 2017, we realized that the executable environment containing all of HIV-TRACE's dependency stack was unwieldy and difficult to use. To solve this problem, we replicated the data workflow in Javascript, enabling MicrobeTrace to perform all of the above steps in a single environment. This transition came at a performance cost. Because HIV-TRACE can access the machine on which it's running more-or-less directly, it can perform certain operations much more rapidly.
MicrobeTrace brings other substantial advantages to the table. Instead of a complex (error-prone) installation process with multiple dependencies, MicrobeTrace is a website. To load it, simply visit the URL. Furthermore, HIVTRACE is used on the command-line, which is confusing and difficult (if not frightening) for non-technical users. MicrobeTrace is a Graphical User Interface which is designed to guide the user gently through every step of the process. Finally, MicrobeTrace's output is also graphical. MicrobeTrace shows you a network, where HIVTrace merely outputs a statistical description of it, and a network file (which MicrobeTrace can open, BTW).
While MicrobeTrace analysis is available through the browser, HIV-TRACE is available through a server. DataMonkey. Some jurisdictions have access to Secure HIV-TRACE, which is a secure version of HIV-Trace
GHOST, or the global hepatitis outbreak and surveillance technology
NextFlu and NextStrain
MicrobeTrace is the only platform which pairs a premium on ease-of-use with data security guarantees. For the non- or semi-technical analyst, it's more feature-full than any other molecular epidemiology platform presently available.