APECS - FTP site for Ian McConnell's MAPLE programs.
Code to Compute Heights on Elliptic Curves - Magma implementation of Silverman's algorithm to compute the canonical height on an elliptic curve over a number field or function field, by Martine Girard.
EIS - Software for computing Fourier coefficients of Eisenstein series attached to lattices by M. Kuss and J. Bruinier. Binaries for x86-Linux.
Ellipsa - Includes Primo, an implementation of ECPP, and CPG, class polynomial builder.
Heegner Tools - Peter Green's Heegner Points package. Requires Linux and Pari/GP 2.1.1 or higher.
Modular Forms Software - HECKE can be used to compute basis of q-expansions and Hecke operators on fairly general spaces of modular forms.
Modular Quaternion Groups - Fundamental domains for Shimura curves, written in GAP. Documented with description of algorithms used and program structure, input and output. Results for quaternion algebras with discriminant up to 100.
Periods of Hilbert Modular Forms - A package of PARI programs (v.2.1.1 or higher) for calculations described in "Periods of Hilbert modular forms and rational points on elliptic curves" by H. Darmon and A. Logan.
TECC - Tiny Elliptic Curve Calculator, by Masanari Kida. Requires KASH 2.2.
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