Cargando…

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling

BACKGROUND: The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scalin...

Descripción completa

Detalles Bibliográficos
Autores principales:	Pelé, Julien, Bécu, Jean-Michel, Abdi, Hervé, Chabbert, Marie
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2012
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403911/ https://www.ncbi.nlm.nih.gov/pubmed/22702410 http://dx.doi.org/10.1186/1471-2105-13-133

Ejemplares similares

Multidimensional Scaling Reveals the Main Evolutionary Pathways of Class A G-Protein-Coupled Receptors
por: Pelé, Julien, et al.
Publicado: (2011)

caOmicsV: an R package for visualizing multidimensional cancer genomic data
por: Zhang, Hongen, et al.
Publicado: (2016)

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves
por: Sprouffske, Kathleen, et al.
Publicado: (2016)

Focused multidimensional scaling: interactive visualization for exploration of high-dimensional data
por: Urpa, Lea M., et al.
Publicado: (2019)

BioShell-Threading: versatile Monte Carlo package for protein 3D threading
por: Gniewek, Pawel, et al.
Publicado: (2014)

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications
por: Chaudhuri, Rima, et al.
Publicado: (2015)

rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects
por: Geerts, Manon, et al.
Publicado: (2021)

geneHummus: an R package to define gene families and their expression in legumes and beyond
por: Die, Jose V., et al.
Publicado: (2019)

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
por: Kaleb, Klara, et al.
Publicado: (2019)

morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring
por: Wagner, Ines, et al.
Publicado: (2014)

OrthoInspector: comprehensive orthology analysis and visual exploration
por: Linard, Benjamin, et al.
Publicado: (2011)

OrthoFinder: phylogenetic orthology inference for comparative genomics
por: Emms, David M., et al.
Publicado: (2019)

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
por: Schreiber, Fabian, et al.
Publicado: (2009)

POInT(browse): orthology prediction and synteny exploration for paleopolyploid genomes
por: Siddiqui, Mustafa, et al.
Publicado: (2023)

eNetXplorer: an R package for the quantitative exploration of elastic net families for generalized linear models
por: Candia, Julián, et al.
Publicado: (2019)

Fragman: an R package for fragment analysis
por: Covarrubias-Pazaran, Giovanny, et al.
Publicado: (2016)

hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups
por: Ferdosi, Mohammad H, et al.
Publicado: (2014)

Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly
por: Wcisel, Dustin J., et al.
Publicado: (2020)

rCUR: an R package for CUR matrix decomposition
por: Bodor, András, et al.
Publicado: (2012)

perfectphyloR: An R package for reconstructing perfect phylogenies
por: Karunarathna, Charith B., et al.
Publicado: (2019)

dna: An R package for differential network analysis
por: Gill, Ryan, et al.
Publicado: (2014)

An R package for analyzing and modeling ranking data
por: Lee, Paul H, et al.
Publicado: (2013)

GENLIB: an R package for the analysis of genealogical data
por: Gauvin, Héloïse, et al.
Publicado: (2015)

micropan: an R-package for microbial pan-genomics
por: Snipen, Lars, et al.
Publicado: (2015)

Visualizing tumor evolution with the fishplot package for R
por: Miller, Christopher A., et al.
Publicado: (2016)

FELLA: an R package to enrich metabolomics data
por: Picart-Armada, Sergio, et al.
Publicado: (2018)

stpm: an R package for stochastic process model
por: Zhbannikov, Ilya Y., et al.
Publicado: (2017)

microclass: an R-package for 16S taxonomy classification
por: Liland, Kristian Hovde, et al.
Publicado: (2017)

iGTP: A software package for large-scale gene tree parsimony analysis
por: Chaudhary, Ruchi, et al.
Publicado: (2010)

inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons
por: Liang, Chunguang, et al.
Publicado: (2006)

ExOrthist: a tool to infer exon orthologies at any evolutionary distance
por: Márquez, Yamile, et al.
Publicado: (2021)

csdR, an R package for differential co-expression analysis
por: Pettersen, Jakob P., et al.
Publicado: (2022)

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems
por: Smith, Robert W., et al.
Publicado: (2018)

AMDA: an R package for the automated microarray data analysis
por: Pelizzola, Mattia, et al.
Publicado: (2006)

WGCNA: an R package for weighted correlation network analysis
por: Langfelder, Peter, et al.
Publicado: (2008)

RankAggreg, an R package for weighted rank aggregation
por: Pihur, Vasyl, et al.
Publicado: (2009)

A flexible R package for nonnegative matrix factorization
por: Gaujoux, Renaud, et al.
Publicado: (2010)

GSAR: Bioconductor package for Gene Set analysis in R
por: Rahmatallah, Yasir, et al.
Publicado: (2017)

wtest: an integrated R package for genetic epistasis testing
por: Sun, Rui, et al.
Publicado: (2019)

ggroups: an R package for pedigree and genetic groups data
por: Nilforooshan, Mohammad Ali, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_kvfat3u883k4khlpo253bcg2pl