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MultiMSOAR specifications


Unique identifier OMICS_16623
Name MultiMSOAR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained No


No version available


This tool is not available anymore.

Publications for MultiMSOAR

MultiMSOAR citations


The gene family free median of three

PMCID: 5446766
PMID: 28559921
DOI: 10.1186/s13015-017-0106-z

[…] 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

PLoS One
PMCID: 4138177
PMID: 25137074
DOI: 10.1371/journal.pone.0105015

[…] 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

PLoS One
PMCID: 3647064
PMID: 23667537
DOI: 10.1371/journal.pone.0062892

[…] 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

Brief Bioinform
PMCID: 3178058
PMID: 21705766
DOI: 10.1093/bib/bbr040

[…] 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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MultiMSOAR institution(s)
Department of Computer Science, University of California Riverside, Riverside, CA, USA
MultiMSOAR funding source(s)
Supported by National Science Foundation grant IIS-0711129.

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