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Phylonet
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List of PhyloNet Commands
CalGTProb Command
CalIntroRate
Charnet Command
Cmpnets Command
CountCoal Command
DeepCoalCount_network
DeepCoalCount_tree Command
ExploreHypothesis_GibbsSampling
GenCplex Command
GenST Command
HmmCommand
Infer_ST_Bootstrap Command
Infer_ST_DV Command
Infer_ST_GLASS Command
Infer_ST_MC Command
Infer_ST_MDC_Time Command
Infer_ST_MDC_UR Command
Infer_ST_MDC Command
InferNetwork_ML
InferNetwork_ML_Bootstrap
InferNetwork_ML_CV Command
InferNetwork_MP
InferNetwork_MPL
LCA Command
MAST Command
MCMC_BiMarkers
MCMC_GT
MCMC_SEQ
MLE_BiMarkers
Multilocus Data
NetMerger
ProcessGT Command
Referring gene trees
RIATAHGT Command
SimBiMarkersinNetwork
SimGTinNetwork Command
SummarizeMCMCResults
SymmetricDifference Command
SummarizeNetworks
VI_coalHMM
DeepCoalCount_AlloppNet
InferNetwork_MP_Allopp
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List of PhyloNet Commands
Page Information
Title:
List of PhyloNet Commands
Author:
Robert Barnett
Feb 20, 2012
Last Changed by:
Zhi Yan
Sep 25, 2020
Tiny Link:
(useful for email)
https://wiki.rice.edu/confluence/x/iptP
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Steinberg, Ethan Hannan (1)
Page:
HmmCommand
Phylonet (31)
Page:
GenST Command
Page:
SimGTinNetwork Command
Page:
Infer_ST_MDC Command
Page:
LCA Command
Page:
MAST Command
Page:
PhyloNet 3 General Overview
Page:
HmmCommand
Page:
DeepCoalCount_tree Command
Page:
Infer_ST_Bootstrap Command
Page:
ExploreHypothesis_GibbsSampling
Page:
Infer_ST_DV Command
Page:
Infer_ST_GLASS Command
Page:
Infer_ST_MDC_Time Command
Page:
Infer_ST_MC Command
Page:
InferNetwork_ML_Bootstrap
Page:
GenCplex Command
Page:
RIATAHGT Command
Page:
InferNetwork_MPL
Page:
InferNetwork_ML_CV Command
Page:
CountCoal Command
Page:
DeepCoalCount_AlloppNet
Page:
Charnet Command
Page:
InferNetwork_MP_Allopp
Page:
CalGTProb Command
Page:
Infer_ST_MDC_UR Command
Page:
SymmetricDifference Command
Page:
ProcessGT Command
Page:
InferNetwork_MP
Page:
Cmpnets Command
Page:
InferNetwork_ML
Page:
DeepCoalCount_network
Hierarchy
Parent Page
Home page:
Home
Children (42)
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
Show all...
Page:
HmmCommand
Page:
Infer_ST_Bootstrap Command
Page:
Infer_ST_DV Command
Page:
Infer_ST_GLASS Command
Page:
Infer_ST_MC Command
Page:
Infer_ST_MDC_Time Command
Page:
Infer_ST_MDC_UR Command
Page:
Infer_ST_MDC Command
Page:
InferNetwork_ML
Page:
InferNetwork_ML_Bootstrap
Page:
InferNetwork_ML_CV Command
Page:
InferNetwork_MP
Page:
InferNetwork_MPL
Page:
LCA Command
Page:
MAST Command
Page:
MCMC_BiMarkers
Page:
MCMC_GT
Page:
MCMC_SEQ
Page:
MLE_BiMarkers
Page:
Multilocus Data
Page:
NetMerger
Page:
ProcessGT Command
Page:
Referring gene trees
Page:
RIATAHGT Command
Page:
SimBiMarkersinNetwork
Page:
SimGTinNetwork Command
Page:
SummarizeMCMCResults
Page:
SymmetricDifference Command
Page:
SummarizeNetworks
Page:
VI_coalHMM
Page:
DeepCoalCount_AlloppNet
Page:
InferNetwork_MP_Allopp
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Recent Changes
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Sep 25, 2020 11:35
Zhi Yan
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Sep 04, 2020 15:21
Xinhao Liu
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Sep 04, 2020 15:17
Xinhao Liu
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Sep 13, 2019 13:26
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Outgoing Links
External Links (27)
https://wiki.rice.edu/confluence/display/PHYLONET/Summarize…
https://wiki.rice.edu/confluence/display/PHYLONET/DeepCoalC…
https://wiki.rice.edu/confluence/display/PHYLONET/MCMC_GT
https://wiki.rice.edu/confluence/display/PHYLONET/CalIntroR…
https://academic.oup.com/bioinformatics/article/35/14/i370/…
https://bmcgenomics.biomedcentral.com/articles/10.1186/s128…
https://wiki.rice.edu/confluence/display/PHYLONET/InferNetw…
ieeexplore.ieee.org/document/4564437/
https://wiki.rice.edu/confluence/display/PHYLONET/InferNetw…
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471…
https://wiki.rice.edu/confluence/display/PHYLONET/MCMC_SEQ
https://wiki.rice.edu/confluence/display/PHYLONET/InferNetw…
https://bioinfocs.rice.edu/node/306
journals.plos.org/plosgenetics/article?id=10.1371/journal.p…
https://link.springer.com/chapter/10.1007/11533719_11
https://www.biorxiv.org/content/biorxiv/early/2018/03/27/28…
biorxiv.org/content/early/2017/04/26/095539
https://wiki.rice.edu/confluence/display/PHYLONET/MCMC_BiMa…
https://academic.oup.com/sysbio/article/62/5/738/1685537/Pa…
https://wiki.rice.edu/confluence/display/PHYLONET/InferNetw…
https://bioinfocs.rice.edu/PhyloNet
onlinelibrary.wiley.com/doi/10.1111/mec.13544/abstract
online.liebertpub.com/doi/abs/10.1089/cmb.2011.0174
journals.plos.org/ploscompbiol/article?id=10.1371/journal.p…
biorxiv.org/content/early/2017/05/29/143545
biorxiv.org/content/early/2016/12/19/095539
www.pnas.org/content/111/46/16448
Phylonet (29)
Page:
GenCplex Command
Page:
NetMerger
Page:
CalGTProb Command
Page:
InferNetwork_ML_CV Command
Page:
Cmpnets Command
Page:
Charnet Command
Page:
ExploreHypothesis_GibbsSampling
Page:
MLE_BiMarkers
Page:
Infer_ST_Bootstrap Command
Page:
Infer_ST_MDC_Time Command
Page:
Infer_ST_MDC Command
Page:
HmmCommand
Page:
DeepCoalCount_tree Command
Page:
CountCoal Command
Page:
SimGTinNetwork Command
Page:
RIATAHGT Command
Page:
VI_coalHMM
Page:
DeepCoalCount_network
Page:
MAST Command
Page:
Infer_ST_GLASS Command
Page:
LCA Command
Page:
InferNetwork_ML_Bootstrap
Page:
Infer_ST_MDC_UR Command
Page:
ProcessGT Command
Page:
SimBiMarkersinNetwork
Page:
Infer_ST_DV Command
Page:
GenST Command
Page:
SymmetricDifference Command
Page:
Infer_ST_MC Command
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