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PhyCLIP is an integer linear programming (ILP) approach that optimally delineates a tree into statistically-principled clusters. Minimally, apart from a rooted phylogeny, 3 additional inputs are required from the user:
- Minimum number of sequences (S) that can be quantified as a cluster.
- Multiple of deviations (gamma) from the grand median of the mean pairwise sequence patristic distance that defines the within-cluster divergence limit.
- False discovery rate (FDR) to infer that the diversity observed for every combinatorial pair of output clusters is significantly distinct from one another.
A manuscript describing PhyCLIP (version 1.0) is published in Molecular Biology and Evolution:
Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
Alvin Xiaochuan Han, Edyth Parker, Frits Scholer, Sebastian Maurer-Stroh, Colin Russell
Molecular Biology and Evolution, msz053; doi: https://doi.org/10.1093/molbev/msz053
We highly encourage that you go through this documentation before starting your analysis.
However, if you would like to promptly run PhyCLIP using the recommended procedure, you may go to:
- Quickstart for beginners - for those who are new or unfamiliar with terminal/command prompt operations.
- Quickstart for advanced users
Contents:
I-a. Quickstart for beginners
I-b. Quickstart for advanced users
II. Installation
III. Usage guide
IV. Output files
V. Optimising input parameters
VI. Prior clusters
VII. Troubleshoot