We present the Uppsala Persian Dependency Treebank (UPDT) with a syntactic annotation scheme based on Stanford Typed Dependencies. The treebank consists of 6,000 sentences and 151,671 tokens with an average sentence length of 25 words. The data is from different genres, including newspaper articles and fiction, as well as technical descriptions and texts about culture and art, taken from the open source Uppsala Persian Corpus (UPC). The syntactic annotation scheme is extended for Persian to include all syntactic relations that could not be covered by the primary scheme developed for English. In addition, we present open source tools for automatic analysis of Persian containing a text normalizer, a sentence segmenter and tokenizer, a part-of-speech tagger, and a parser. The treebank and the parser have been developed simultaneously in a bootstrapping procedure. The result of a parsing experiment shows an overall labeled attachment score of 82.05% and an unlabeled attachment score of 85.29%. The treebank is freely available as an open source resource.