SDM specifications

Information


Unique identifier OMICS_24958
Name SDM
Alternative name Super Distance Matrix
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for Super Distance Matrix

SDM in publications

 (8)
PMCID: 3986248
PMID: 24732341
DOI: 10.1371/journal.pone.0094279

[…] distance for each taxa pair from multiple genes. in their method, estimated distances are weighted according to their level of uncertainty. the weights are based on a given substitution model . the super distance matrix (sdm) computes a single scale coefficient for each distance matrix, as well as external branch length correction coefficient for each taxon inside each considered gene […]

PMCID: 3348158
PMID: 22590545
DOI: 10.1371/journal.pone.0036443

[…] was observed. the highest-likelihood tree thus identified was taken as the 6-gene best ml phylogenetic hypothesis for subsequent analyses. the corresponding phylograms were subjected to the super-distance matrix (sdm) approach to estimate the relative substitution rate among 12s rdna, 16s rdna, coxi, cyb, rho and rag1., node stability was estimated under ml through 400 replicates […]

PMCID: 3249592
PMID: 22229028
DOI: 10.1155/2011/524182

[…] present an extensive simulation study comparing the performance of mrp and the polynomial supertree methods mincut supertree, modified mincut supertree, build-with-distances, physic, physic_ist, and super distance matrix. we consider both quality and resolution of the reconstructed supertrees. our findings illustrate the tradeoff between accuracy and running time in supertree construction, […]

PMCID: 3154253
PMID: 21853022
DOI: 10.1371/journal.pone.0021915

[…] by model selection since trn+i+γ, gtr+γ, or the model-averaged option available in jmodeltest give identical topologies., second, we built supertrees from the individual gene trees using the super distance matrix (sdm) method, which normalises tree lengths before combining the trees; this is less sensitive to rate heterogeneity than the first method . we then imported the supermatrix […]

PMCID: 3142523
PMID: 21702931
DOI: 10.1186/1471-2148-11-181

[…] distances between individual loci and the multigenic trees (d(ts, fj) in equation 2) to relevant phylogenetic parameters, including alignment length, average evolutionary rate (estimated with the super-distance matrix method []), and shape parameter α of the gamma distribution (obtained in ml analyses of individual loci). we also tested if incongruences were positively correlated […]


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SDM institution(s)
Groupe Phylogenie Moleculaire, ISEM, Universite Montpellier 2, Montpellier, France ; Equipe Methodes et Algorithmes pour la Bioinformatique, LIRMM (CNRS, Universite Montpellier 2), Montpellier, France
SDM funding source(s)
Supported by ACI Informatique, Mathematique et Physique en Biologie Moleculaire (ACI IMP-Bio), and by IFR119 Biodiversity Continentale Mediterraneenne et Tropicale (Montpellier) computing facilities.

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