SEADOG
SEADOG 1.0 and SEADOG-ILP 1.0
SEADOG (short for “Simultaneous Evolutionary Analysis of DOmains and Genes through phylogenetic reconciliation”) and SEADOG-ILP (short for “SEADOG using Integer Linear Programming”) are software packages for simultaneous inference of domain-level and gene-level evolution through a joint phylogenetic reconciliation of domain, gene, and species trees. Both software take as input a rooted or unrooted domain tree, rooted gene trees for the gene families in which the domains of the domain tree occur, and a rooted species tree on the species considered in the analysis.
SEADOG implements a heuristic algorithm for estimating optimal 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. Further details on the functionality of SEADOG 1.0 appear in the manual, and a description of the heuristic it implements is available in the paper “An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution” listed below.
SEADOG-ILP implements an exact, ILP-based algorithm for computing optimal Domain-Gene-Species reconciliations in either a biologically restricted or unrestricted search space. SEADOG-ILP can output all optimal Domain-Gene-Species reconciliations in its search space and often produces more optimal reconciliations that the heuristic implemented in SEADOG. However, SEADOG-ILP is not as scalable as SEADOG. Further details on the functionality of SEADOG-ILP 1.0 appear in its manual, and a description of the exact algorithm it implements is available in the paper “An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem” listed below. Note that SEADOG-ILP must be compiled locally by the user so it can be properly linked to the CPlex solver and has only been tested on Linux.
Both SEADOG and SEADOG-ILP are available open source under GPL version 3, but without any guarantee of correctness.
A prototype version of an extended version of SEADOG, called SEADOG-MD (short for SEADOG Multi-Domain), is also available below. SEADOG-MD allows for the simultaneous reconciliation of multiple domain trees with multiple gene trees and a species tree.
SEADOG 1.0 (beta version) download and manual
- Executables for: Linux, Mac
- Source code: SEADOG (available open source under GNU GPL version 3)
- Manual: pdf
- Sample data set: Test Data
SEADOG 1.0 implements algorithms described in the following manuscript:
- An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution
Lei Li, Mukul S. Bansal.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB); 16(1): 63-76, 2019.
Supplementary material for this paper is available here.
SEADOG-ILP 1.0 download and manual
- Source code: SEADOG-ILP (available open source under GNU GPL version 3)
- Installation instructions and Manual: pdf
- Sample data set: Test Data
SEADOG-ILP 1.0 implements algorithms described in the following manuscript:
- An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem
Lei Li, Mukul S. Bansal.
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2018; Proceedings, pages 386-397.
SEADOG-MD (prototype) download and manual
SEADOG-MD implements the heuristic described in the following manuscript:
- Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model
Lei Li, Mukul S. Bansal.
ISBRA 2019; LNCS 11490: 73-86.
Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation award IIS 1553421.
Contact: Please feel free to contact Mukul Bansal (mukul.bansal@uconn.edu) if you have any questions, concerns, or suggestions.