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MultiMSOAR specifications

Information


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

Versioning


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Maintainer


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Publications for MultiMSOAR

MultiMSOAR citations

 (4)
library_books

The gene family free median of three

2017
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 []. […]

library_books

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

2014
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 […]

library_books

The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

2013
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 […]

library_books

Positional orthology: putting genomic evolutionary relationships into context

2011
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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