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Found 33 Software Packages (Results 1–33)

ape

Software Authors:   Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,Christoph Heibl, Daniel Lawson, Vincent Lefort, PierreLegendre, Jim Lemon, Yvonnick Noel, Johan Nylander, RainerOpgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, KorbinianStrimmer, Damien de Vienne
Cited in: 53 Publications (2004–2022)
Related Software: R; phytools; GEIGER; MrBayes; phangorn; cluster (R); …
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

PhyloNetwork

Software Authors:   Gabriel Cardona, Francesc Rosselló, Gabriel Valiente
Cited in: 24 Publications (2010–2022)
Related Software: bioperl; NetDiversity; PERL; PADRE; TOPD/FMTS; GitHub; …
Main Fields: Combinatorics (05-XX); Order, lattices, ordered algebraic structures (06-XX); Computer science (68-XX)

DendroPy

Software Authors:   Sukumaran, J.; Mark T. Holder
Cited in: 6 Publications (2017–2022)
Related Software: Biopython; Python; RAxML; INDELible; ASTRAL-II; ETE; …
Main Fields: General and overarching topics; collections (00-XX); Linear and multilinear algebra; matrix theory (15-XX); Statistics (62-XX)

Phyloseq

Software Authors:   Paul J. McMurdie; Susan Holmes
Cited in: 5 Publications (2015–2021)
Related Software: R; ggplot2; GUniFrac; shiny; vegan; multtest; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

pplacer

Software Authors:   Matsen, F.A., R.B. Kodner, et al.
Cited in: 7 Publications (2002–2022)
Related Software: MLTreeMap; SEPP; TIPP; FastTree; DEPP; PhyloGeoTool; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

SackinMinimizer

Software Authors:   Fischer, Mareike
Cited in: 7 Publications (2020–2021)
Related Software: OEIS; Mathematica; R; SymmeTree; GitHub; devtools; …
Main Fields: Combinatorics (05-XX); Measure and integration (28-XX); Biology and other natural sciences (92-XX)

TreeFix

Software Authors:   Wu, Y., Rasmussen, M., Bansal, M., Kellis, M.
Cited in: 7 Publications (2013–2021)
Related Software: ecceTERA; Notung; RAxML; PHYLIP; OCTAL; FastMe; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Statistics (62-XX)

BEAGLE

Software Authors:   Ayres, D.L., Darling, A., Zwickl, D.J., Beerli, P., Holder, M.T., Lewis, P.O., Huelsenbeck, J.P., Ronquist, F., Swofford, D.L., Cummings, M.P., Rambaut, A., Suchard, M.A.
Cited in: 4 Publications (2014–2022)
Related Software: R; BEAST; MrBayes; BEAUti; ape; Rcpp; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

Bio++

Software Authors:   Dutheil J, Boussau B
Cited in: 3 Publications (2011–2019)
Related Software: ExaBayes; MulRF; iGTP; MrBayes; SplitsTree; pIQPNNI; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Operations research, mathematical programming (90-XX)

Hetero

Software Authors:   Jermiin LS, Ho SYW, Ababneh F et al
Cited in: 5 Publications (2006–2017)
Related Software: PHYLIP; R; ape; S-PLUS; Seq-Gen; fastDNAml; …
Main Fields: History and biography (01-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

HyPhy

Software Authors:   Kosakovsky Pond SL, Frost SDW, Muse SV
Cited in: 2 Publications (2017–2020)
Related Software: Datamonkey; Python; phyphy; CodonTest; ALF; xREI; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

MOLPHY

Software Authors:   Adachi, J., Hasegawa, M.
Cited in: 4 Publications (2002–2019)
Related Software: PHYLIP; fastDNAml; ExaBayes; ExaML; MulRF; iGTP; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

PHYLO_WIN

Software Authors:   Galtier N, Gouy M, Gautier C
Cited in: 2 Publications (2010–2017)
Related Software: SEAVIEW; CINEMA; Jalview; UniProt; PHYLIP; Tracer; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

Phylomatic

Software Authors:   Webb, C.O.; Donoghue, M.J.
Cited in: 4 Publications (2010–2017)
Related Software: ape; R; EstimateS; PhD; SpadeR; iNEXT
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

SEAVIEW

Software Authors:   Galtier N, Gouy M, Gautier C
Cited in: 2 Publications (2010–2017)
Related Software: PHYLO_WIN; CINEMA; Jalview; UniProt; PHYLIP; Tracer; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

MultiPhyl

Software Authors:   Keane TM, Naughton TJ, McInerney JO
Cited in: 2 Publications (2010–2015)
Related Software: PAML; apTreeshape; R; ACME; ClustalW; Algorithm 97; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BIO Phylo

Software Authors:   Vos, R.A.; Caravas, J.; Hartmann, K.; Jensen, M.A.; Miller, C.
Cited in: 1 Publication (2017)
Related Software: PERL; ape; FairShapley; GEIGER; bioperl; phytools; …
Main Fields: Biology and other natural sciences (92-XX)

FlipCut

Software Authors:   Brinkmeyer, Malte; Griebel, Thasso; B"ocker, Sebastian
Cited in: 2 Publications (2011–2013)
Related Software: RAxML; Rec-I-DCM3; SuperTriplets; PhySIC; EPoS; PAUP*
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

MorphoJ

Software Authors:   Klingenberg, Christian Peter
Cited in: 1 Publication (2016)
Related Software: R; shapes; geomorph; ape; ade4; Momocs; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

numecolR

Software Authors:   Borcard, Daniel; Gillet, François; Legendre, Pierre
Cited in: 2 Publications (2011–2018)
Related Software: ape; vegan; spdep; MVPARTwrap; mvpart; labdsv; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

UShER

Software Authors:   Turakhia, Y., et al.
Cited in: 2 Publications (2002–2022)
Related Software: DEPP; PhyloGeoTool; INSTRAL; HmmUFOtu; MLTreeMap; SEPP; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

BayesCAT

Software Authors:   Shim, Heejung; Larget, Bret
Cited in: 1 Publication (2018)
Related Software: SATe; Bali-phy; Statalign
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BoundedCoalescent

Software Authors:   Carson, Jake; Ledda, Alice; Ferretti, Luca; Keeling, Matt; Didelot, Xavier
Cited in: 1 Publication (2022)
Related Software: phyloscanner; phylodyn; SimPhy; Rcpp; ape; R
Main Fields: Biology and other natural sciences (92-XX)

DAMBE7

Software Authors:   Xuhua Xia
Cited in: 1 Publication (2020)
Related Software: CodonTest; ALF; xREI; RevTrans; MACSE; EasyCodeML; …
Main Fields: Biology and other natural sciences (92-XX)

FISHtrees

Software Authors:   Gertz, E.M., Chowdhury, S.A., Lee, W., Wangsa, D., Heselmeyer-Haddad, K., Ried, T., Schwartz, R., Schäffer, A.A.
Cited in: 1 Publication (2019)
Related Software: ExaBayes; ExaML; MulRF; iGTP; GASTS; MLGO; …
Main Fields: General and overarching topics; collections (00-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

gromovlab

Software Authors:   Volkmar Liebscher
Cited in: 1 Publication (2018)
Related Software: ape; distory; lpSolve; lp_solve; R
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

phylotools

Software Authors:   Jinlong Zhang, Nancai Pei, Xiangcheng Mi
Cited in: 1 Publication (2018)
Related Software: BASECO; Phylocom; ape; R
Main Fields: Biology and other natural sciences (92-XX)

SDSparsimony

Software Authors:   Gilks, Walter R.; Wang, Chinying
Cited in: 1 Publication (2011)
Related Software: R
Main Fields: Biology and other natural sciences (92-XX)

SINATRA

Software Authors:   Wang, Bruce; Sudijono, Timothy; Kirveslahti, Henry; Gao, Tingran; Boyer, Douglas M.; Mukherjee, Sayan; Crawford, Lorin
Cited in: 1 Publication (2021)
Related Software: Morpho; ShapeWorks; SECT; FastGP; Rvcg; gglasso; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

TreeSwift

Software Authors:   N. Moshiri
Cited in: 0 Publications
Related Software: TreeN93; TreeCluster; FAVITES; PhyloSift; ETE; DendroPy; …
Main Fields:

Triplet MaxCut

Software Authors:   Sevillya, G., Frenkel, Z., Snir, S.
Cited in: 1 Publication (2019)
Related Software: ExaBayes; ExaML; MulRF; iGTP; GASTS; MLGO; …
Main Fields: General and overarching topics; collections (00-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

PAL

Software Authors:   Alexei Drummond, Korbinian Strimmer
Cited in: 0 Publications
Related Software:
Main Fields:

rwty

Software Authors:   Dan Warren, Anthony Geneva, Rob Lanfear
Cited in: 0 Publications
Related Software:
Main Fields: