SAMBA: Super Area-cladogram after resolving Multiple Biogeographical Ambiguities

Aim: Cladistic biogeography is all about congruence: when individual area cladograms coincide, they result in a general area cladogram that reveals shared history. However, the complexities of the natural world hamper the reconstruction of fully solved biogeographical patterns. Herein, we present SAMBA (Super Area-cladogram after resolving Multiple Biogeographical Ambiguities), a pattern-based method combining supertrees and area cladograms to depict the relationships among areas. We also present a prototypical implementation of SAMBA as a web-based framework named iSAMBA.
Location: Global
Taxon: Any taxon can be analyzed with SAMBA
Methods: SAMBA is based on phylogenetic supertrees, a technique that combines previously calculated phylogenetic trees to produce a general area cladogram representing conciliatory and non-ambiguous patterns of relationships. In our method, the input topologies are individual area cladograms. SAMBA is implemented through a web-based framework named iSAMBA. W..., Please see the README document (\"README_dm\") and the accompanying paper: Santos, D., Sampronha, S., Hammoud, H., Gois, J.P. & Santos, C.M.D. 2023. SAMBA: Super Area-cladogram after resolving Multiple Biogeographical Ambiguities. Journal of Biogeography. Accepted. We implemented SAMBA as a web-based framework named iSAMBA. It is freely available at http://nuvem.ufabc.edu.br/isamba. The input for iSAMBA is a set of individual area cladograms in parenthetical format. After uploading a text file with the input area cladograms, iSAMBA generates the MRP-combined matrix, making it available to download in “.nex” and “.ss” files format. The MRP-combined matrix can be analyzed in any software that performs parsimony analysis. The result is the super area-cladogram., This dataset contains the iSAMBA tool's code, the instructions to run it locally, the input tree files used in the scenarios described in the paper, and the resulting matrices for each scenario after SAMBA (formats .ss and .nex).
The iSAMBA tool is freely available online (http://nuvem.ufabc.edu.br/isamba)