RAMI, a software for clustering, visualization, plotting and index creation
The software takes a newick file as input alternatively a nexus (or altnex) tree file created in PAUP. It clusters adjacent sequences as outlined in the forthcoming paper "RAMI, a new tool to characterize microdiverse clusters in microbial communities: application to ribosomal DNA sequences from the marine environment" by Pommier, T., Canbäck, B., Lundberg, P. Hagström. Å & Tunlid, A. The software also produces six different indices explained below and in more detail in the paper.
- Xdistance The average patristic distance between OTUs in a cluster
- Xdepth,nearest The average patristic distance between OTUs and the nearest ancestral node in the cluster
- Xdepth,deepest The average patristic distance to the deepest node in the cluster
- Ydistance The average patristic distance between a cluster and other clusters in the tree
- Ydepth,nearest The patristic distance between a cluster and the nearest ancestral node in the cluster
- Ydepth,deepest The average patristic distance to the deepest node in the tree
There are several software for clustering sequences. Typically these use sequence distance based algorithms. The advantage of using RAMI is that it uses branch lengths (patristic distances) to produce the clusters. With RAMI it is the user that decides which tree reconstruction algorithm that should be used. With the aid of the iTOL online software, clustering may be visualized.
To understand the cluster definition used here, please see the following link. A more detailed explanation of the indices is shown here.
RAMI is written in PERL by Björn Canbäck. RAMI is provided as is. Code will be available after publication.