Linguistic corpus annotation is one of the most important phases for solving Natural Language Processing (NLP) tasks, as these methods are deeply involved with corpus-based techniques. However, meta-data annotation is a highly laborious manual task. A supportive alternative requires the use of computational tools. They are likely to simplify some of these operations, while can be adjusted appropriately to the needs of particular language features at the same time. Therefore, this paper presents ChAnot, a web-based annotation tool developed for Peruvian indigenous and highly agglutinative languages, where Shipibo-Konibo was the case study. This new tool is able to support a diverse set of linguistic annotation tasks, such as word segmentation, POS-tag markup, among others. Also, it includes a suggestion engine based on historic and machine learning models, and a set of statistics about previous annotations.