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  1. Abstract We complete the computation of all$$\mathbb {Q}$$ Q -rational points on all the 64 maximal Atkin-Lehner quotients$$X_0(N)^*$$ X 0 ( N ) such that the quotient is hyperelliptic. To achieve this, we use a combination of various methods, namely the classical Chabauty–Coleman, elliptic curve Chabauty, quadratic Chabauty, and the bielliptic quadratic Chabauty method (from a forthcoming preprint of the fourth-named author) combined with the Mordell-Weil sieve. Additionally, for square-free levelsN, we classify all$$\mathbb {Q}$$ Q -rational points as cusps, CM points (including their CM field andj-invariants) and exceptional ones. We further indicate how to use this to compute the$$\mathbb {Q}$$ Q -rational points on all of their modular coverings. 
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  2. Building on Mazur’s 1978 work on prime degree isogenies, Kenku determined in 1981 all possible cyclic isogenies of elliptic curves over Q \mathbb {Q} . Although more than 40 years have passed, the determination of cyclic isogenies of elliptic curves over a single other number field has hitherto not been realised. In this paper we develop a procedure to assist in establishing such a determination for a given quadratic field. Executing this procedure on all quadratic fields Q ( d ) \mathbb {Q}(\sqrt {d}) with | d | > 10 4 |d| > 10^4 we obtain, conditional on the Generalised Riemann Hypothesis, the determination of cyclic isogenies of elliptic curves over 19 19 quadratic fields, including Q ( 213 ) \mathbb {Q}(\sqrt {213}) and Q ( −<#comment/> 2289 ) \mathbb {Q}(\sqrt {-2289}) . To make this procedure work, we determine all of the finitely many quadratic points on the modular curves X 0 ( 125 ) X_0(125) and X 0 ( 169 ) X_0(169) , which may be of independent interest. 
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  3. We describe how the quadratic Chabauty method may be applied to determine the set of rational points on modular curves of genus$$g>1$$whose Jacobians have Mordell–Weil rank$$g$$. This extends our previous work on the split Cartan curve of level 13 and allows us to consider modular curves that may have few known rational points or non-trivial local height contributions at primes of bad reduction. We illustrate our algorithms with a number of examples where we determine the set of rational points on several modular curves of genus 2 and 3: this includes Atkin–Lehner quotients$$X_0^+(N)$$of prime level$$N$$, the curve$$X_{S_4}(13)$$, as well as a few other curves relevant to Mazur's Program B. We also compute the set of rational points on the genus 6 non-split Cartan modular curve$$X_{\scriptstyle \mathrm { ns}} ^+ (17)$$. 
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