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Publications for MultiMSOAR
The gene family free median of three
[…] 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 . […]
Orthology Detection Combining Clustering and Synteny for Very Large Datasets
[…] 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 […]
The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships
[…] 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 […]
Positional orthology: putting genomic evolutionary relationships into context
[…] 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 […]
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