Information

ARMADiLLO stands for “Antigen Receptor Mutation Analyzer for Detection of Low-Likelihood Occurrences” and is used for calculating the probability of amino acid mutations of antibody sequence. ARMADiLLO identifies improbable antibody mutations that are not routinely targeted by the somatic hypermutation machinery during B cell maturation. The science behind ARMADiLLO is described in the 2018 paper by Wiehe et. al.. This web application provides an interface to the ARMADiLLO stand alone program along with UCA calculations provided by Cloanalyst. (In the advanced options, it is possible to supply a custom UCA or calculate the UCA using the alternate program Partis.) Running and inspecting the results of this web application can be found in the Help section. This web application has been tested on multiple operating systems and web browsers as shown below.

OS	Version	Chrome	Firefox	Microsoft Edge	Safari
Linux	Mint 20.2	108.0	107.0	n/a	n/a
MacOS	Monterey	108.0	102.5	n/a	16.1
Windows	10	108.0	107.0	108.0	n/a

The code for ARMADiLLO can be found on github. The ARMADiLLO application is a C++, command line application that performs the mutations that provides that backend processing of the ARMADiLLO website. It requires the C++ boost library to compile. We recommend the Cloanalyst package for determining the UCA; however, ARMADiLLO will accept a fasta containing the UCA independent of how the UCA is generated. We have bundled everything needed to run a standalone version of ARMADiLLO into a container that is available upon request at . The detailed documentation for ARMADiLLO can be found at read-the-docs.

If you use this website please cite the following papers:

• Martin Beem JS, Venkatayogi S, Haynes BF, Wiehe K. (2023) ARMADiLLO: a web server for analyzing antibody mutation probabilities. Nucleic Acids Res. 2023;gkad398. doi:10.1093/nar/gkad398.
• Wiehe K., Bradley T., Meyerhoff R.R., Hart C. Williams W.B., Easterhoff D., Faison W.J., Kepler T.B., Saunders K.O., Alam S.M., Bonsignori M. and Haynes B.F. (2018) Functional Relevance of Improbable Antibody Mutations for HIV Broadly Neutralizing Antibody Development. Cell Host & Microbe. 23(6):759-765.

If Partis is used to generate the UCA, please cite the associated Partis paper:

• Ralph DK, Matsen FA. (2019) Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data. PLoS Comput Biol 15(7): e1007133. https://doi.org/10.1371/journal.pcbi.1007133.

Copyright Notice

The copyrights of this software are owned by Duke University. As such, two licenses for this software are offered:
1. An open-source license under the CC BY-NC-ND 4.0 license for non-commercial academic use.
2. A custom license with Duke University, for commercial use or uses without the CC BY-NC-ND 4.0 license restrictions.

As a recipient of this software, you may choose which license to receive the code under. Outside contributions to the Duke-owned code base cannot be accepted unless the contributor transfers the copyright to those changes over to Duke University. To enter a custom license agreement without the the CC BY-NC-ND 4.0 license restrictions, please contact the Digital Innovations department at the Duke Office for Translation & Commercialization (OTC) at otcquestions@duke.edu with reference to “OTC File No. 5124” in your email.

Please note that this software is distributed AS IS, WITHOUT ANY WARRANTY; and without the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.