Laboratoire Bordelais de Recherche en Informatique UMR 5800 - Universit´ e Bordeaux 1, 351, cours de la Lib´ eration, 33405 Talence cedex, France Research Report RR-1443-08 New algorithms for aligning nested arc-annotated sequences by A¨ ıda Ouangraoua, Cedric Chauve, Valentin Guignon and Sylvie Hamel April, 2008