====== Available Extensions ======

''polymake'' supports an [[user_guide:extend:extensions|extension system]] for writing and maintaining outside the distribution.  Please contact the extension's authors if you have questions.

===== Lattice Polytopes and Toric Geometry =====

  * Silke Horn/Andreas Paffenholz:
    * //[[https://github.com/apaffenholz/polymake_flint_wrapper|polymake_flint_wrapper]]// Computation of Hermite Normal Form, Smith Normal Form and LLL-reduced lattice bases using the [[http://flintlib.org/|flint]] library

  * Andreas Paffenholz:
    * //[[https://github.com/apaffenholz/polymake_LatticeNormalForm|LatticeNormalForm]]// Normal forms of lattice polytopes and lattice equivalence of lattice polytopes
    * //[[https://github.com/apaffenholz/polymake_ntl_wrapper|ntl_wrapper]]//: This extension provides a small interface to lll and lets you compute an lll-reduced lattice basis and a basis of the integer relations of the rows of a matrix.
    * //[[https://github.com/apaffenholz/polymake_polyhedral_adjunction|polyhedral_adjunction]]//: This extension provides properties and constructions used in [[http://arxiv.org/abs/1105.2415|DiRocco, Haase, Nill, Paffenholz: Polyhedral Adjunction Theory, arxiv:1105:2415]]. In particular, it computes the nef value and the Q-codegree of a polytope.

===== Tropical Geometry =====
  * Ewgenij Gawrilow, Michael Joswig, Benjamin Schröter: [[extensions:polytropes|polytropes]]
  * Alheydis Geiger and Marta Panizzut: [[extensions:tropicalquarticcurves|TropicalQuarticCurves]]
  * Michael Joswig, Marta Panizzut, Bernd Sturmfels: [[extensions:tropicalcubics|Tropical Cubics]]
  * Simon Hampe: [[https://github.com/simonhampe/atint|Algorithmic tropical intersection theory]] (now bundled with polymake)
  * Silke Horn: [[http://solros.de/polymake/tropmat/|Tropical Oriented Matroids]]
===== Integer Programming =====

  * Matthias Walter: With [[http://github.com/xammy/unimodularity-test/wiki/Polymake-Extension|this extension]] you can test an integer matrix for total unimodularity. If the answer is "no", it can return the row/column indices of a submatrix with |det| >= 2. It can also test for the related properties (strong) unimodularity, (strong) k-modularity and the Dantzig property. See [[http://matthiaswalter.org/TUtest/|here]] for more information on implementation and theory.

===== Extended Formulations =====

  * Matthias Walter: [[https://github.com/xammy/polymake-extended-formulations|This extension]] can compute nonnegative slack matrix factorizations from extended formulations of polytopes and vice versa. See [[https://github.com/xammy/polymake-extended-formulations/wiki|here]] for more information.

===== Phylogenetics =====

  * Sven Herrmann: [[https://www.uea.ac.uk/groups-and-centres/computational-biology/software/quasidec|QuasiDec]]. This extension contains an algorithm for computing the block decomposition of a quasi-median graph obtained from a set of partitions or a sequence alignment.
  * Sven Herrmann and Andreas Spillner: [[https://www.uea.ac.uk/groups-and-centres/computational-biology/software/comrit|CoMRiT]]. This extensions contains a new application metric introducing finite metric spaces as objects. The core feature is an algorithm to compute a realisation of a finite metric space using the tight-span, as described in Herrmann, Moulton, Spillner: Computing Realizations of Finite Metric Spaces.