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Protocols

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

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Publication for Super Distance Matrix

SDM citations

 (9)
library_books

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

2017
Viruses
PMCID: 5408678
PMID: 28387730
DOI: 10.3390/v9040072

[…] tractive option for large data sets, where they can provide a snapshot of the underlying evolutionary relationships quickly and easily. A species tree was constructed from all gene matrices using the super distance matrix (SDM) approach—method weighted by alignment lengths []. A balanced minimum evolution tree was inferred from the resulting distance supermatrix by FastME (fast minimum evolution) […]

library_books

Combining Distance Matrices on Identical Taxon Sets for Multi Gene Analysis with Singular Value Decomposition

2014
PLoS One
PMCID: 3986248
PMID: 24732341
DOI: 10.1371/journal.pone.0094279

[…] e 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 so that t […]

call_split

A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes

2012
PLoS One
PMCID: 3348158
PMID: 22590545
DOI: 10.1371/journal.pone.0036443
call_split See protocol

[…] ikelihood 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 of boots […]

call_split

Polynomial Supertree Methods Revisited

2011
Adv Bioinformatics
PMCID: 3249592
PMID: 22229028
DOI: 10.1155/2011/524182
call_split See protocol

[…] ilar to ACS, the distance-based method SDM uses a more involved standardization procedure and is able to use both sequences and gene trees as input (See [] for details). The possibly still incomplete super distance matrix is then processed using MRV* (a variant of minimum variance reduction), BioNJ* or NJ* (variants of neighbor-joining) []. […]

library_books

Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene

2011
PLoS One
PMCID: 3154253
PMID: 21853022
DOI: 10.1371/journal.pone.0021915

[…] t affected 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 of s […]

call_split

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

2011
BMC Evol Biol
PMCID: 3142523
PMID: 21702931
DOI: 10.1186/1471-2148-11-181
call_split See protocol

[…] let 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 with recombin […]


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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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