Search queries have evolved beyond keyword queries. Many complex queries such as verbose queries, natural language question queries and document-based queries are widely used in a variety of applications. Processing these complex queries usually requires a series of query operations, which results in multiple sequences of reformulated queries. However, previous query representations, either the "bag of words" method or the recently proposed "query distribution" method, cannot effectively model these query sequences, since they ignore the relationships between two queries. In this paper, a reformulation tree framework is proposed to organize multiple sequences of reformulated queries as a tree structure, where each path of the tree corresponds to a sequence of reformulated queries. Specifically, a two-level reformulation tree is implemented for verbose queries. This tree effectively combines two query operations, i.e., subset selection and query substitution, within the same framework. Furthermore, a weight estimation approach is proposed to assign weights to each node of the reformulation tree by considering the relationships between different nodes and directly optimizing retrieval performance. Experiments on TREC collections show that this reformulation tree based representation significantly outperforms the state-of-the-art techniques.