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: 55 Publications (2004–2022) Related Software: R; phytools; ggplot2; GEIGER; MrBayes; phangorn; … Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Probability theory and stochastic processes (60-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: iGTP; ExaBayes; MulRF; 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; CodonPhyML; ntCard; ACUA; … 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; iGTP; Bio++; UFBoot2; ExaBayes; … 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; iGTP; TOPAL; … 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; iGTP; TOPAL; … 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: PhySIC; RAxML; Rec-I-DCM3; SuperTriplets; 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: CodonPhyML; ntCard; ACUA; PAML; CodonTest; ALF; … 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: iGTP; Bio++; UFBoot2; ExaBayes; ExaML; MulRF; … 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: iGTP; Bio++; UFBoot2; ExaBayes; ExaML; MulRF; … 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: –