SEADOG-Gen is a software package for joint phylogenetic reconciliation of domain, gene, and species trees for microbial species. It takes as input a rooted domain tree, one or more rooted gene trees (corresponding to the gene families in which the domains of the domain tree are found), and a rooted species tree for the microbial species considered in the analysis. SEADOG-Gen implements two heuristic algorithms for estimating optimal Generalized Domain-Gene-Species reconciliations, i.e., it outputs a reconciliation of the domain tree with the gene trees and of the gene trees with the species tree while allowing for domain duplication, domain transfer (inter/intra species as well as within/across gene families), domain loss, gene duplication, gene transfer, and gene loss. SEADOG-Gen assumes that both domain transfer and gene transfer can occur easily in the species being analyzed, and the implemented algorithms only work well under this assumption. For Domain-Gene-Species reconciliation in the context of non-microbial species (without frequent horizontal transfer) we recommend using the previously published SEADOG software package instead. Further details on the functionality of SEADOG-Gen appear in the manual, and a description of the heuristic it implements is available in the paper listed below.
SEADOG-Gen was implemented by Abhijit Mondal. The software is available open source under GPL version 3, but without any guarantee of correctness.
SEADOG-Gen 1.0 download and manual
- Executable (JAR file) and source code (Java): SEADOG-Gen.zip (available open source under GNU GPL version 3)
- Manual: SEADOG-Gen_Manual.pdf
SEADOG-Gen implements algorithms described in the following manuscript:
- Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains
Abhijit Mondal, Mukul S. Bansal
IEEE/ACM Transactions on Computational Biology and Bioinformatics; in press.
Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation award IIS 1553421.