SOcial and PHilogenetic Investigation of Epidemics
Main function: AMNetCons = inferTransNetSOPHIE(filePhylo,nSamp,degDistrType,degDistr,transRate,consType,enforceTree,visualize)
Input paramers:
- filePhylo - name of file with the phylogenetic tree (in Newick or Nexus formats)
- nSamp - number of samples from the joint distribution of ancestral label assignments
- degDistrType - type of random contact network degree distribution. possible variants: 'power law', 'custom'
- degDistr - exponent of the power law contact network degree distribution (if degDistrType = 'power law') or actual distribution (if degDistrType = 'custom')
- transRate - transmission rate (used in Jukes-Cantor trait substitution model)
- consType - the likelihood used to build a consensus transmission tree. Variants: 'joint' (default), 'phylogenetic', 'network'
- enforceTree - whether to force algorithm to consider only sampled acyclic transmission networks. Variants: 0 (default), 1
- visualize - whether to output a figure with the inferred transmission network. Default value: 0
Output:
AMNetCons - adjacency matrix of the inferred transmission network
The example of tool execution can be found in exampleRun.m
Implementation of Edmonds algorithm for maximal arborescence is taken from https://www.mathworks.com/matlabcentral/fileexchange/24899-edmonds-algorithm Copyright (c) 2009, Ashish Choudhary. All rights reserved.
You can find the python version under "sophie_python" folder.