Open-source Software.

tao

The package that can be described is not the tao package.

pomp

Inference for partially-observed Markov processes (POMPs).

phylopomp

R package for partially observed Markov genealogy processes

PartiallyObservedMarkovProcesses.jl

Julia port of pomp.

panelPomp

R package for statistical inference using panel POMPs.

spatPomp

R package for statistical inference on spatiotemporal POMP models.

ouch

Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses.

subplex

The subplex optimization algorithm in R.

Mathematica Addons

Mathematica packages for normal forms, ideal theory, continuation of bifurcations, multivariate Taylor series, and other calculations.

NormalForm

A Mathematica package for computing normal forms of vectorfields using Lie series. Also contains VFTransform, a function for transforming vectorfields.

BifCurve

A Mathematica package for continuation of bifurcations.

Taylor

A Mathematica package for multivariable Taylor series expansions.

Frechet

A Mathematica package implementing multivariable differentiation.

Ideal

A Mathematica package for commutative algebra.

Prof. King on github