We calculate the impact of the intergalactic medium (IGM) on the observed Lyman alpha lines (hereafter Lya) emitted by galaxies in an ionised IGM at z>4. Our model accounts for gas clumping in the IGM and for the fact that high-redshift galaxies reside in overdense regions, which causes the velocity field of the IGM to depart from the Hubble flow. The observed shape of the Lya line varies widely, with dependence on the intrinsic width and systemic velocity of the line, a galaxies star formation rate and the local extra-galactic UV-background. For large star formation rates and levels of the UV-background, absorption in the IGM does not result in a Lya line that is asymmetric as is common among known high-redshift Lya emitters. For models in which the lines do show the observed strong asymmetry, the IGM typically transmits only 10-30% of the Lya flux. The increase in the ionising background that accompanied the completion of reionisation barely increased the IGM transmission, which suggests that LAEs of comparable luminosity should not appear to be significantly dimmer prior to overlap. In this light, we briefly discuss the potential of Lya emitters as a probe into the epoch of reionisation.
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