MultiMSOAR

[…] GB memory and a time limit of 1 h per dataset. In both simulated and real data we set the FFAdj-3G’s parameter α to 0.9.In our experiments, we compare ourselves against the orthology prediction tool MultiMSOAR []. This tool requires precomputed gene families, which we constructed by following the workflow described in []. […]

[…] tant sequence data.A large class of orthology detection tools therefore attempts to explicitly infer gene phylogenies and their reconciliation with species trees, e.g. Orthology analysis using MCMC , MultiMSOAR , LOFT , Ensembl Compara , and Synergy . Although this tree-based approach is often considered the most accurate, it suffers from high computational costs and is hence limited in practice t […]

[…] values for the subcluster or clades within the cluster are not considered in this decision process. Other orthology prediction programs using such a bottom-up approach are, e.g., OrthoMCL, ReMark or MultiMSOAR 2.0 , , .Both procedures are very rigid in their orthology prediction, but in theory both can still erroneously assign paralogous sequences into a single ortholog cluster. This is due to th […]

[…] llowing SOAR, MSOAR [] was developed to additionally model duplications, translocations and chromosomal fusions and fissions. MSOAR 2.0 [] improved on MSOAR by handling tandem duplication events, and MultiMSOAR [] and MultiMSOAR 2.0 [] extended these methods to multiple genomes. Algorithms and challenges of the parsimony approach to orthology prediction were recently reviewed [].The advantages of […]