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Description

Download PhyloNet

  • The method can summarize common structures with their proportion from networks based on your selected summarizing mode.
  • Input: a set of networks (with their proportion) that have the same taxa, 
  • Output: a set of common structures with their proportions.

 

Usage

 

SummarizeNetworks networks mode [-n] [-o]



networksComma delimited list of networks to summarize.mandatory

mode

a number in {1,2,3,4,5}.

1: displayed trees.

2: backbone networks.

3: tree decomposition.

4: tripartition.

5: major trees. If the input networks only contain topologies without inheritance probabilities, the user should not use this mode.

mandatory

-nif specified, normalize input networks proportion, make their summation to be 1. Default value is false, which means no normalization.optional

-o outputFile

if specified, the output file is outputFile. The default outputFile is SummarizeNetworks.txt under the user's directory.

optional

Examples

Input networks have proportions.

Download: wheatExample.nex

Please don't copy and paste, since some illegal characters might be copied.

#NEXUS
 
BEGIN NETWORKS;
 
Network net1=[&W 0.33]((((Ash,(At,TaD)))X#H1,Y#H2),((((Asp,TaB),X#H1),((TaA,Tu),Tm)))Y#H2); 
Network net2=[&W 0.33]((((Ash,(At,TaD)))X#H1,((Asp,TaB),((((TaA,Tu),Tm),X#H1))Y#H2)),Y#H2);
Network net3=[&W 0.2]((((((Ash,(At,TaD)))X#H1,((Asp,TaB))Y#H2),((TaA,Tu),Tm)),X#H1),Y#H2);
Network net4=[&W 0.07]((((((Ash,(At,TaD)))X#H1,((Asp,TaB))Y#H2),((TaA,Tu),Tm)),Y#H2),X#H1);
Network net5=[&W 0.05]((((Ash,(At,TaD)))X#H1,((Asp,TaB))Y#H2),(((TaA,Tu),Tm),(X#H1,Y#H2)));
END;
BEGIN PHYLONET;
 
SummarizeNetworks (net1,net2,net3,net4,net5) 2 -n;
 
END;

 

 

Input networks don't have proportions.

Download: mpl4Sum.nex

Please don't copy and paste, since some illegal characters might be copied.

#NEXUS
 
BEGIN NETWORKS;
Network net1=((L:1.0)#H1:1.0::0.6775044779684056,((F:1.0,((K:1.0,(P:1.0)#H3:1.0::0.6753614616352684):1.1244258148662702)#H2:1.5700202905515581::0.6135769094686397):5.938615025704547,(((#H1:1.0::0.3224955220315944)#H4:1.0::0.7475384042289634,(#H2:5.938905009947807::0.38642309053136026,(C:1.0,#H4:1.0::0.2524615957710365):5.913620320644154):5.912120605817229):5.94018448223261,(#H3:1.0::0.32463853836473155,O:1.0):2.8047977192873814):5.903825230963656):5.93953170330228);
Network net2=((L:1.0)#H1:1.0::0.697819639034568,((F:1.0,((K:1.0,(P:1.0)#H3:1.0::0.6745110428348149):1.1100661168406565)#H2:1.7082666741217403::0.6142669809548641):5.931845445367439,((#H3:1.0::0.3254889571651851,O:1.0):2.4833570014727955,(#H2:5.929217003496626::0.3857330190451359,((#H1:1.0::0.302180360965432)#H4:1.0::0.017142685450424855,(C:1.0,#H4:1.0::0.9828573145495751):5.91361935198872):5.9135981328244815):5.925654204620761):5.9260404685243415):5.937215530824061);
Network net3=((L:1.0)#H1:1.0::0.697176914245199,(((((K:1.0,(P:1.0)#H3:1.0::0.6779314464962011):1.0884181724604034)#H2:5.934653324530301::0.38618142938381267,(C:1.0,#H1:1.0::0.302823085754801):5.9084237144406755):5.9397822589449465,((#H3:1.0::0.3220685535037989)#H4:1.0::0.017142685450424855,(#H4:1.0::0.9828573145495751,O:1.0):0.00808293691880342):2.7714903993551276):5.904173024132873,(#H2:2.012640927894127::0.6138185706161874,F:1.0):5.904657745927051):5.937801402829414);
Network net4=((L:1.0)#H1:1.0::0.6712728892686329,(((#H1:1.0::0.32872711073136707,(((K:1.0,(P:1.0)#H3:1.0::0.6751112732063029):1.1267080674211265)#H2:5.938355167858189::0.38140833857114587,C:1.0):5.911170667122007):5.939107582827078,(#H3:1.0::0.32488872679369707,O:1.0):2.860440724320893):5.926093346898221,(F:1.0,#H2:1.6125835293541366::0.6185916614288541):5.9381572434685745):5.939517506695277);
Network net5=((L:1.0)#H1:1.0::0.6966745198922524,((F:1.0,(((P:1.0)#H3:1.0::0.683073175568802,K:1.0):1.0524332659314857)#H2:2.5623058987490537::0.6104433712226643):5.906687726566634,((#H3:1.0::0.316926824431198,O:1.0):3.4112578018682806,(#H2:5.937243226797915::0.38955662877733566,(C:1.0,#H1:1.0::0.3033254801077477):5.909482135710924):5.909111928318673):5.9042519002108):5.9371033552041155);
END;
BEGIN PHYLONET;
 
SummarizeNetworks (net1,net2,net3,net4,net5) 1 -n;
 
END;

 

Command References

  1. Zhen Cao, Xinhao Liu, Huw A. Ogilvie, Zhi Yan, and Luay Nakhleh. Practical Aspects of Phylogenetic Network Analysis Using PhyloNet. 


See Also

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