Title: List of PhyloNet Commands  
Author:Barnett, Robert Matthew Feb 20, 2012
Last Changed by:Cao, Zhen Sep 13, 2019
Tiny Link: (useful for email) https://wiki.rice.edu/confluence/x/iptP
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Steinberg, Ethan Hannan (1)
    Page: HmmCommand
Phylonet (29)
    Page: RIATAHGT Command
    Page: ExploreHypothesis_GibbsSampling
    Page: InferNetwork_ML
    Page: LCA Command
    Page: CalGTProb Command
    Page: Infer_ST_MC Command
    Page: DeepCoalCount_tree Command
    Page: SymmetricDifference Command
    Page: HmmCommand
    Page: Infer_ST_MDC Command
    Page: InferNetwork_MP
    Page: Infer_ST_GLASS Command
    Page: ProcessGT Command
    Page: Infer_ST_MDC_Time Command
    Page: Infer_ST_DV Command
    Page: PhyloNet 3 General Overview
    Page: MAST Command
    Page: InferNetwork_ML_Bootstrap
    Page: GenCplex Command
    Page: DeepCoalCount_network
    Page: Infer_ST_MDC_UR Command
    Page: InferNetwork_MPL
    Page: SimGTinNetwork Command
    Page: Cmpnets Command
    Page: CountCoal Command
    Page: GenST Command
    Page: Charnet Command
    Page: Infer_ST_Bootstrap Command
    Page: InferNetwork_ML_CV Command
Hierarchy
Parent Page
    Home page: Home
Children (39)
    Page: CalGTProb Command
    Page: CalIntroRate
    Page: Charnet Command
    Page: Cmpnets Command
    Page: CountCoal Command
    Page: DeepCoalCount_network
    Page: DeepCoalCount_tree Command
    Page: ExploreHypothesis_GibbsSampling
    Page: GenCplex Command
    Page: GenST Command
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Outgoing Links
External Links (24)
    https://www.biorxiv.org/content/biorxiv/early/2018/03/27/28…
    onlinelibrary.wiley.com/doi/10.1111/mec.13544/abstract
    https://bmcgenomics.biomedcentral.com/articles/10.1186/s128…
    online.liebertpub.com/doi/abs/10.1089/cmb.2011.0174
    biorxiv.org/content/early/2017/05/29/143545
    https://wiki.rice.edu/confluence/display/PHYLONET/InferNetw…
    www.pnas.org/content/111/46/16448
    https://bmcgenomics.biomedcentral.com/articles/10.1186/1471…
    https://academic.oup.com/sysbio/article/62/5/738/1685537/Pa…
    journals.plos.org/plosgenetics/article?id=10.1371/journal.p…
    https://wiki.rice.edu/confluence/display/PHYLONET/InferNetw…
    https://link.springer.com/chapter/10.1007/11533719_11
    https://bioinfocs.rice.edu/PhyloNet
    https://wiki.rice.edu/confluence/display/PHYLONET/MCMC_GT
    biorxiv.org/content/early/2016/12/19/095539
    https://wiki.rice.edu/confluence/display/PHYLONET/MCMC_BiMa…
    biorxiv.org/content/early/2017/04/26/095539
    https://wiki.rice.edu/confluence/display/PHYLONET/MCMC_SEQ
    https://wiki.rice.edu/confluence/display/PHYLONET/Summarize…
    https://wiki.rice.edu/confluence/display/PHYLONET/CalIntroR…
    journals.plos.org/ploscompbiol/article?id=10.1371/journal.p…
    https://wiki.rice.edu/confluence/display/PHYLONET/InferNetw…
    ieeexplore.ieee.org/document/4564437/
    https://bioinfocs.rice.edu/node/306
Phylonet (28)     Page: DeepCoalCount_network
    Page: Infer_ST_GLASS Command
    Page: Cmpnets Command
    Page: GenST Command
    Page: CountCoal Command
    Page: CalGTProb Command
    Page: Infer_ST_MDC Command
    Page: InferNetwork_ML_CV Command
    Page: NetMerger
    Page: MLE_BiMarkers
    Page: ProcessGT Command
    Page: Charnet Command
    Page: MAST Command
    Page: Infer_ST_Bootstrap Command
    Page: GenCplex Command
    Page: Infer_ST_MC Command
    Page: RIATAHGT Command
    Page: Infer_ST_DV Command
    Page: Infer_ST_MDC_Time Command
    Page: SimGTinNetwork Command
    Page: HmmCommand
    Page: ExploreHypothesis_GibbsSampling
    Page: SimBiMarkersinNetwork
    Page: Infer_ST_MDC_UR Command
    Page: DeepCoalCount_tree Command
    Page: LCA Command
    Page: SymmetricDifference Command
    Page: InferNetwork_ML_Bootstrap