RAPPAS — Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences — is software for the phylogenetic identification of gene sequences, usually obtained by recovering DNA material from environmental samples (e.g. from soil, water or human samples such as saliva or feces). Starting from a phylogenetic tree showing the known relationships between a group of organisms (e.g. a family of viruses, a clade of bacteria, etc.), RAPPAS solves the task of placing each sequence inside this tree, thus revealing the precise evolutionary origin of the organisms contained in the environmental sample.
The typical use of RAPPAS is the detection, monitoring and analysis of biodiversity. For example, to characterize communities of microorganisms such as the human microbiome and its relationship with disease, diet and various traits. In a viral context, RAPPAS can be used to determine the identity of viral sequences in a dataset, as this can have important implications for predicting disease progression, resistance to antiviral drugs or the ability to evade the immune system.
From a methodological point of view, the originality of RAPPAS lies in the fact that it performs all the heavy evolutionary modeling calculations at a pre-processing stage. This information is stored in a large data structure which is then queried at the analysis stage, allowing very rapid identification of the sequences in the sample and avoiding a well-known bottleneck in bioinformatics analysis, the alignment of sequences.
Reference: B. Linard, K. Swenson, F. Pardi. Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinformatics 35 (18): 3303-3312 (2019)