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adj2pajek.m
adj2pajekEdgeTypes.m
align.m
align_IgnoreGaps.m
calcAncestries.m
calcConsensus.m
calcLabelsPhyloTree.m
calcTimeSamp_MJNSimul.m
calc_centroids.m
calculate_P_info.m
eListToAM.m
eListToAM_matr.m
estimateHubs.m
findDSampDir.m
findDSampDir1.m
findTransNetMCMC4.m
findTransNetMCMC5.m
getDegDistr.m
grow.m
growBaB.m
growBaB1.m
growBaB2.m
isConnected.m
isprocess.m
modifyTree.m
modifyTree1.m
objTransNetPhyloFit2.m
objTransNetPhyloFit3.m
objTransNetPhyloFit4.m
objTransNetQuadDeg2.m
outbreaks_aspen1.m
outbreaks_aspen_run.m
parsave.m
parsePIDsWin.m
quentin.m
quentin_run.m
readNEXUS2.m
readSeqFreq.m
readme.md
recalcUniques.m
sCore.m
saveMJNet.m
saveNEXUS.m
saveNEXUSSplitsTree.m
saveparfor.m
simOutbreak.m
simulEvol.m
simulEvol1.m
treeAM.m
treeAMdirect.m
treeDM.m
treeDMdirect.m
treeToTransNet.m

readme.md

Welcome to the QUENTIN wiki!

This repository contains the version of QUENTIN implemented in matlab. QUENTIN is also available in python, see

https://github.com/walkergussler/quentin

The description below is about matlab version. The main script is called quentin.m Input/output format:

[HostNetThr, sources, transNets,transTrees] = quentin(inputFolder,splitsTreeFolder,distType,distThr,nclust,nIterSimul,nIterMCMC,nInstMCMC,interHostCoeffs,rho)

Input parameters:

inputFolder is a folder with input files in fasta format. All sequenced should be aligned splitsTreeFolder is a folder, where SplitsTree is located (could be downloaded at http://www.splitstree.org/) distType - type of genetic distance used by the algorithm. Possible types: [] (default value), 'evol' (simulation-based distance described in the paper), 'consensus' (distance between consensuses), 'mindist' (minimal distance between populations). Default value: 'evol' distThr - distance threshold for transmission clusters detection nclust - number of intra-host variants in each population, to which all populations are reduced to eliminate sampling bias. If nclust = [], then the default value nclust = 12 is used nIterSimul - maximal number of iterations for viral evolution simulation nIterMCMC - maximal number of iterations for MCMC algorithm nInstMCMC - number of parallel instances of MCMC interHostCoeffs - range of values for the coefficient (\alpha)^{-1} for the estimation of likelihood of genetic distances. If interHostCoeffs = [], then the default value interHostCoeffs = [1 1.25 1.5] is used rho - range of values for the coefficient \rho for prior probability of transmission tree estimation. If rho = [], then the default value rho = 1 is used Output:

HostNetThr - graph obtained from the host network by removal of arcs with weights exceeding the threshold. Weakly connected components of this graph are transmission clusters sources - sources of outbreaks for all transmission clusters transNets - transmission networks for all transmission clusters transTrees - transmission trees for all transmission clusters Example:

inputFolder = 'AA_clipped';

splitsTreeFolder = 'SplitsTree';

distThr = 1100;

nIterSimul = 3000;

nIterMCMC = 250;

nInstMCMC = 4;

[HostNetThr, sources, transNets,TransTrees] = quentin(inputFolder,splitsTreeFolder,[],distThr, [],nIterSimul,nIterMCMC,nInstMCMC,[],[]);