├── .classpath ├── .project ├── LICENSE.txt ├── README.md ├── Tutorial ├── CMoutput │ ├── 1inputFile │ │ ├── clustInfo_1_20.28.csv │ │ ├── dataSet1_Cluster31.figTree │ │ ├── dataSet1_Cluster32.figTree │ │ ├── dataSet1_Cluster40.figTree │ │ ├── dataSet1_Cluster43.figTree │ │ └── log_2012-6-14_20.28.txt │ └── 2inputFiles │ │ ├── clustInfo_3_20.38.csv │ │ ├── dataSet1_Cluster1.figTree │ │ ├── dataSet1_Cluster11.figTree │ │ ├── dataSet1_Cluster14.figTree │ │ ├── dataSet1_Cluster15.figTree │ │ ├── dataSet1_Cluster17.figTree │ │ ├── dataSet1_Cluster18.figTree │ │ ├── dataSet1_Cluster22.figTree │ │ ├── dataSet1_Cluster23.figTree │ │ ├── dataSet1_Cluster24.figTree │ │ ├── dataSet1_Cluster25.figTree │ │ ├── dataSet1_Cluster26.figTree │ │ ├── dataSet1_Cluster28.figTree │ │ ├── dataSet1_Cluster29.figTree │ │ ├── dataSet1_Cluster3.figTree │ │ ├── dataSet1_Cluster30.figTree │ │ ├── dataSet1_Cluster31.figTree │ │ ├── dataSet1_Cluster32.figTree │ │ ├── dataSet1_Cluster34.figTree │ │ ├── dataSet1_Cluster40.figTree │ │ ├── dataSet1_Cluster42.figTree │ │ ├── dataSet1_Cluster43.figTree │ │ ├── dataSet1_Cluster44.figTree │ │ ├── dataSet1_Cluster45.figTree │ │ ├── dataSet1_Cluster46.figTree │ │ ├── dataSet1_Cluster48.figTree │ │ ├── dataSet1_Cluster49.figTree │ │ ├── dataSet1_Cluster5.figTree │ │ ├── dataSet1_Cluster51.figTree │ │ ├── dataSet1_Cluster53.figTree │ │ ├── dataSet1_Cluster55.figTree │ │ ├── dataSet1_Cluster6.figTree │ │ ├── dataSet1_Cluster64.figTree │ │ ├── dataSet1_Cluster66.figTree │ │ ├── dataSet1_Cluster67.figTree │ │ ├── dataSet1_Cluster68.figTree │ │ ├── dataSet1_Cluster69.figTree │ │ ├── dataSet1_Cluster7.figTree │ │ ├── dataSet1_Cluster70.figTree │ │ ├── dataSet1_Cluster71.figTree │ │ ├── dataSet1_Cluster9.figTree │ │ └── log_2012-6-14_20.38.txt ├── CPoutput │ ├── EU1866 │ │ ├── EU1866.treeforCPT_clusterPicks.nwk │ │ ├── EU1866.treeforCPT_clusterPicks.nwk.figTree │ │ ├── EU1866.treeforCPT_clusterPicks_log.txt │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks.fas │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster12_sequenceList.txt │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster31_sequenceList.txt │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster32_sequenceList.txt │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster40_sequenceList.txt │ │ └── EU1866_EU1866.treeforCPT_clusterPicks_cluster43_sequenceList.txt │ └── EU3031 │ │ ├── EU3031.treeforCPT_clusterPicks.nwk │ │ ├── EU3031.treeforCPT_clusterPicks.nwk.figTree │ │ ├── EU3031.treeforCPT_clusterPicks_log.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks.fas │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster101_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster121_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster124_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster138_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster170_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster171_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster178_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster195_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster196_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster202_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster210_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster222_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster224_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster30_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster33_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster52_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster59_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster67_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster76_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster78_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster86_sequenceList.txt │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster90_sequenceList.txt │ │ └── EU3031_EU3031.treeforCPT_clusterPicks_cluster95_sequenceList.txt ├── EU1866.fas ├── EU1866.treeforCPT.nwk ├── EU3031.fas ├── EU3031.treeforCPT.nwk ├── TestDataset_3031_epiData.csv ├── Tutorial_January2016.pdf ├── combine_CPCM.R └── launchCPloop.py ├── _config.yml ├── bin ├── clusterMatcher │ ├── ClusPtr.class │ ├── Main$Task.class │ ├── Main$Task2.class │ ├── Main.class │ ├── ReadInClusters.class │ ├── ReadNewick.class │ ├── SeqNode.class │ └── Wind.class └── clusterPicking │ ├── BasicSequence.class │ ├── BasicSequenceTester.class │ ├── ClusterPicker.class │ ├── ClusterPickerGUI$1.class │ ├── ClusterPickerGUI$2.class │ ├── ClusterPickerGUI$3.class │ ├── ClusterPickerGUI$4.class │ ├── ClusterPickerGUI$DoItJobThread.class │ ├── ClusterPickerGUI$GOActionListener.class │ ├── ClusterPickerGUI$ParameterChangeListener.class │ ├── ClusterPickerGUI$SetFileListener.class │ ├── ClusterPickerGUI$ShowAboutActionListener.class │ ├── ClusterPickerGUI$ShowInstructionsActionListener.class │ ├── ClusterPickerGUI$ShowMissingActionListener.class │ ├── ClusterPickerGUI$UpdateMessage.class │ ├── ClusterPickerGUI.class │ ├── FigTreeWriter.class │ ├── Node.class │ ├── ReadFasta.class │ ├── Tree.class │ ├── TreeReader.class │ ├── TreeTester.class │ ├── TreeWriter.class │ ├── WriteFasta.class │ └── rainbow_256_cols.class ├── combine_CPCM.R ├── docs ├── ClusterMatcher_manual.pdf ├── ClusterPicker1.2_Manual_Sept2015.pdf └── ClusterTutorial │ ├── AvianFlu │ ├── Flu_PB2.nwk │ ├── Flu_PB2_clusterPicks.nwk │ ├── Flu_PB2_clusterPicks.nwk.figTree │ ├── Flu_PB2_clusterPicks_log.txt │ ├── Flu_PB2_unique.Fasta │ └── Flu_PB2_unique.Fasta_Flu_PB2_clusterPicks.fas │ ├── HCV │ ├── 0.7_2 │ │ ├── HCV3876_clusterPicks.nwk │ │ ├── HCV3876_clusterPicks.nwk.figTree │ │ ├── HCV3876_clusterPicks_log.txt │ │ └── HCV_1b_3876_HCV3876_clusterPicks.fas │ ├── 0.9_2 │ │ ├── HCV3876_clusterPicks.nwk │ │ ├── HCV3876_clusterPicks.nwk.figTree │ │ ├── HCV3876_clusterPicks_log.txt │ │ └── HCV_1b_3876_HCV3876_clusterPicks.fas │ ├── HCV3876.nwk │ ├── HCV_1b_3876.fas │ └── HCV_data_3876.csv │ ├── HIV │ ├── CMoutput │ │ ├── 1inputFile │ │ │ ├── clustInfo_1_20.28.csv │ │ │ ├── dataSet1_Cluster31.figTree │ │ │ ├── dataSet1_Cluster32.figTree │ │ │ ├── dataSet1_Cluster40.figTree │ │ │ ├── dataSet1_Cluster43.figTree │ │ │ └── log_2012-6-14_20.28.txt │ │ └── 2inputFiles │ │ │ ├── clustInfo_3_20.38.csv │ │ │ ├── dataSet1_Cluster1.figTree │ │ │ ├── dataSet1_Cluster11.figTree │ │ │ ├── dataSet1_Cluster14.figTree │ │ │ ├── dataSet1_Cluster15.figTree │ │ │ ├── dataSet1_Cluster17.figTree │ │ │ ├── dataSet1_Cluster18.figTree │ │ │ ├── dataSet1_Cluster22.figTree │ │ │ ├── dataSet1_Cluster23.figTree │ │ │ ├── dataSet1_Cluster24.figTree │ │ │ ├── dataSet1_Cluster25.figTree │ │ │ ├── dataSet1_Cluster26.figTree │ │ │ ├── dataSet1_Cluster28.figTree │ │ │ ├── dataSet1_Cluster29.figTree │ │ │ ├── dataSet1_Cluster3.figTree │ │ │ ├── dataSet1_Cluster30.figTree │ │ │ ├── dataSet1_Cluster31.figTree │ │ │ ├── dataSet1_Cluster32.figTree │ │ │ ├── dataSet1_Cluster34.figTree │ │ │ ├── dataSet1_Cluster40.figTree │ │ │ ├── dataSet1_Cluster42.figTree │ │ │ ├── dataSet1_Cluster43.figTree │ │ │ ├── dataSet1_Cluster44.figTree │ │ │ ├── dataSet1_Cluster45.figTree │ │ │ ├── dataSet1_Cluster46.figTree │ │ │ ├── dataSet1_Cluster48.figTree │ │ │ ├── dataSet1_Cluster49.figTree │ │ │ ├── dataSet1_Cluster5.figTree │ │ │ ├── dataSet1_Cluster51.figTree │ │ │ ├── dataSet1_Cluster53.figTree │ │ │ ├── dataSet1_Cluster55.figTree │ │ │ ├── dataSet1_Cluster6.figTree │ │ │ ├── dataSet1_Cluster64.figTree │ │ │ ├── dataSet1_Cluster66.figTree │ │ │ ├── dataSet1_Cluster67.figTree │ │ │ ├── dataSet1_Cluster68.figTree │ │ │ ├── dataSet1_Cluster69.figTree │ │ │ ├── dataSet1_Cluster7.figTree │ │ │ ├── dataSet1_Cluster70.figTree │ │ │ ├── dataSet1_Cluster71.figTree │ │ │ ├── dataSet1_Cluster9.figTree │ │ │ └── log_2012-6-14_20.38.txt │ ├── CPoutput │ │ ├── EU1866 │ │ │ ├── EU1866.treeforCPT_clusterPicks.nwk │ │ │ ├── EU1866.treeforCPT_clusterPicks.nwk.figTree │ │ │ ├── EU1866.treeforCPT_clusterPicks_log.txt │ │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks.fas │ │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster12_sequenceList.txt │ │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster31_sequenceList.txt │ │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster32_sequenceList.txt │ │ │ ├── EU1866_EU1866.treeforCPT_clusterPicks_cluster40_sequenceList.txt │ │ │ └── EU1866_EU1866.treeforCPT_clusterPicks_cluster43_sequenceList.txt │ │ └── EU3031 │ │ │ ├── EU3031.treeforCPT_clusterPicks.nwk │ │ │ ├── EU3031.treeforCPT_clusterPicks.nwk.figTree │ │ │ ├── EU3031.treeforCPT_clusterPicks_log.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks.fas │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster101_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster121_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster124_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster138_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster170_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster171_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster178_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster195_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster196_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster202_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster210_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster222_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster224_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster30_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster33_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster52_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster59_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster67_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster76_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster78_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster86_sequenceList.txt │ │ │ ├── EU3031_EU3031.treeforCPT_clusterPicks_cluster90_sequenceList.txt │ │ │ └── EU3031_EU3031.treeforCPT_clusterPicks_cluster95_sequenceList.txt │ ├── EU1866.fas │ ├── EU1866.nwk │ ├── EU1866.treeforCPT.nwk │ ├── EU3031.fas │ ├── EU3031.nwk │ ├── EU3031.treeforCPT.nwk │ └── TestDataset_3031_epiData.csv │ ├── MCC_to_NWK.R │ ├── PandemicFlu │ ├── CP_results_70_70_002_10 │ │ ├── h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks.nwk │ │ ├── h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks.nwk.figTree │ │ ├── h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_log.txt │ │ ├── h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks.fas │ │ ├── h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_cluster2_sequenceList.txt │ │ ├── h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_cluster3_sequenceList.txt │ │ └── h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_cluster4_sequenceList.txt │ ├── h1n1_pandemic_492_short.fas │ ├── h1n1_pandemic_492_short_beast_mcc.tre │ └── h1n1_pandemic_492_short_beast_mcc.tre.posterior.nwk │ └── SeasonalFlu │ ├── CM_results │ ├── Asia │ │ ├── clustInfo_1_10.30.csv │ │ ├── dataSet1_Cluster2.figTree │ │ ├── dataSet1_Cluster28.figTree │ │ ├── dataSet1_Cluster89.figTree │ │ └── log_2013-9-26_10.30.txt │ └── all_clusters_details │ │ ├── clustInfo_1_10.32.csv │ │ └── log_2013-9-26_10.32.txt │ ├── CP_results_70_70_002_10 │ ├── h3n2_1027_beast_mcc.tre.posterior_clusterPicks.nwk │ ├── h3n2_1027_beast_mcc.tre.posterior_clusterPicks.nwk.figTree │ ├── h3n2_1027_beast_mcc.tre.posterior_clusterPicks_log.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks.fas │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster10_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster13_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster1_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster27_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster28_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster2_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster30_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster41_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster4_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster69_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster70_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster71_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster80_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster87_sequenceList.txt │ ├── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster89_sequenceList.txt │ └── h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster90_sequenceList.txt │ ├── h3n2_1027.fas │ ├── h3n2_1027_beast_mcc.tre │ ├── h3n2_1027_beast_mcc.tre.posterior.nwk │ └── h3n2_1027_traits.csv ├── invisBox.jpg ├── lib ├── about_opencsv_jar.txt └── opencsv-2.3.jar ├── pressIco.jpg ├── release ├── ClustMatch1.2.7.jar ├── ClusterPickerGUI_1.2.5.jar ├── ClusterPicker_1.2.5.jar └── about_the_jars.txt ├── scripts ├── combine_CPCM.R └── launchCPloop.py └── src ├── clusterMatcher ├── ClusPtr.java ├── Main.java ├── ReadInClusters.java ├── ReadNewick.java ├── SeqNode.java └── Wind.java └── clusterPicking ├── BasicSequence.java ├── BasicSequenceTester.java ├── ClusterPicker.java ├── ClusterPickerGUI.java ├── FigTreeWriter.java ├── Node.java ├── ReadFasta.java ├── Tree.java ├── TreeReader.java ├── TreeTester.java ├── TreeWriter.java ├── WriteFasta.java └── rainbow_256_cols.java /.classpath: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -------------------------------------------------------------------------------- /.project: -------------------------------------------------------------------------------- 1 | 2 | 3 | cluster-picker-and-cluster-matcher 4 | 5 | 6 | 7 | 8 | 9 | org.eclipse.jdt.core.javabuilder 10 | 11 | 12 | 13 | 14 | 15 | org.eclipse.jdt.core.javanature 16 | 17 | 18 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## Welcome to ClusterPicker and ClusterMatcher GitHub! 2 | 3 | _Please note these programs are no longer actively maintained (since 2017)_ 4 | 5 | Here you can download all the latest versions of ClusterPicker, ClusterMatcher, and their documentation! 6 | 7 | If you are an advanced user, you may prefer to view this respository on GitHub itself by clicking the blue link at the top of the page. 8 | 9 | If you're just here for the latest jar files to run the programs, we can help you! 10 | 11 | ### Downloads 12 | 13 | #### ClusterPicker 14 | Download the latest ClusterPicker (command-line) [by clicking here](https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/raw/master/release/ClusterPicker_1.2.5.jar). 15 | 16 | Download the latest ClusterPickerGUI (GUI version) [by clicking here](https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/raw/master/release/ClusterPickerGUI_1.2.5.jar). 17 | 18 | Download the ClusterPicker manual [here](https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/raw/master/docs/ClusterPicker1.2_Manual_Sept2015.pdf) 19 | 20 | #### ClusterMatcher 21 | Download the latest ClusterMatcher [by clicking here](https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/raw/master/release/ClustMatch1.2.7.jar). 22 | 23 | Download the ClusterMatcher manual [here](https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/raw/master/docs/ClusterMatcher_manual.pdf) 24 | 25 | ### Documents 26 | 27 | For some information about when the latest jar files were built and how to run them, you can view the text file [here](https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/blob/master/release/about_the_jars.txt). 28 | 29 | To to the [docs folder](https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher/tree/master/docs) to get the lateast manual and tutorial files. 30 | 31 | ### Tutorial 32 | 33 | You can see the files related to a 2016 tutorial in the Tutorial folder -------------------------------------------------------------------------------- /Tutorial/CMoutput/1inputFile/clustInfo_1_20.28.csv: -------------------------------------------------------------------------------- 1 | Clust_ID,Num_Seqs,Madrid,Antwerp,London,BIRMINGHAM,Sampling city_NA,no,yes,Drug naive_NA,SPAIN,BELGIUM,GERMANY,FRANCE,UNITED KINGDOM,GREECE,ITALY,CZECH REPUBLIC,Country_NA,Male Sex with Male,Heterosexual,IV Drug User,Risk factor_NA 2 | 43,5,0,0,0,0,5,3,2,0,0,0,0,0,5,0,0,0,0,4,0,1,0 3 | 40,6,0,0,0,0,6,1,5,0,0,0,0,0,6,0,0,0,0,5,1,0,0 4 | 32,6,0,0,0,0,6,0,6,0,0,0,0,0,6,0,0,0,0,6,0,0,0 5 | 31,5,0,0,0,0,5,4,1,0,0,0,0,0,3,0,2,0,0,5,0,0,0 6 | -------------------------------------------------------------------------------- /Tutorial/CMoutput/1inputFile/log_2012-6-14_20.28.txt: -------------------------------------------------------------------------------- 1 | **Cluster Matcher** 2 | ------------------- 3 | Created 2011 by Emma Hodcroft 4 | Leigh Brown Group, Edinburgh University 5 | ======================================= 6 | 7 | Input files used: 8 | Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU1866\EU1866_clusterPicks.nwk 9 | Annotation file: C:\MyDocuments\Clusters\ClusterTutorial\TestDataset_3031_epiData.csv 10 | Data Set 2: 11 | Newick file: 12 | 13 | The data set had 1866 sequences and 71 clusters (containing 171 sequences (9.16%)) 14 | 15 | 16 | *Preview Analysis* (No files written): 17 | 5 clusters in data set 1 (7.04%) have more than 3 sequences. 18 | 19 | *FigTree Files Written*: 20 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\1inputFile 21 | 5 clusters in data set 1 (7.04%) have more than 3 sequences. 22 | Of these, 4 clusters (5.63%) have at least 1% sequences with a Country value of UNITED KINGDOM 23 | Of the 22 sequences in these clusters: 24 | - 0 (0.0%) are SPAIN 25 | - 0 (0.0%) are BELGIUM 26 | - 0 (0.0%) are GERMANY 27 | - 0 (0.0%) are FRANCE 28 | - 20 (90.91%) are UNITED KINGDOM 29 | - 0 (0.0%) are GREECE 30 | - 2 (9.09%) are ITALY 31 | - 0 (0.0%) are CZECH REPUBLIC 32 | - 0 (0.0%) have no Country value 33 | -------------------------------------------------------------------------------- /Tutorial/CMoutput/2inputFiles/log_2012-6-14_20.38.txt: -------------------------------------------------------------------------------- 1 | **Cluster Matcher** 2 | ------------------- 3 | Created 2011 by Emma Hodcroft 4 | Leigh Brown Group, Edinburgh University 5 | ======================================= 6 | 7 | Input files used: 8 | Data Set 1: 9 | Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU1866\EU1866_clusterPicks.nwk 10 | Annotation file: Will not be used (see '?' below) 11 | Data Set 2: 12 | Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU3031\EU3031_clusterPicks.nwk 13 | Annotation file: C:\MyDocuments\Clusters\ClusterTutorial\TestDataset_3031_epiData.csv 14 | 15 | Data set 1 had 1866 sequences and 71 clusters (containing 171 sequences (9.16%)) 16 | Data set 2 had 3031 sequences and 228 clusters (containing 640 sequences (21.12%)) 17 | 18 | 19 | *Preview Analysis* (No files written): 20 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 21 | Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 1 22 | Of the 103 sequences in the clusters returned from data set 1: 23 | - 0 (0.0%) are SPAIN 24 | - 2 (1.94%) are BELGIUM 25 | - 0 (0.0%) are GERMANY 26 | - 0 (0.0%) are FRANCE 27 | - 97 (94.17%) are UNITED KINGDOM 28 | - 0 (0.0%) are GREECE 29 | - 3 (2.91%) are ITALY 30 | - 1 (0.97%) are CZECH REPUBLIC 31 | - 0 (0.0%) are DENMARK 32 | - 0 (0.0%) are CYPRUS 33 | - 0 (0.0%) have no Country value 34 | Of the 190 sequences in the matching clusters returned from data set 2: 35 | - 0 (0.0%) are SPAIN 36 | - 2 (1.05%) are BELGIUM 37 | - 0 (0.0%) are GERMANY 38 | - 0 (0.0%) are FRANCE 39 | - 178 (93.68%) are UNITED KINGDOM 40 | - 0 (0.0%) are GREECE 41 | - 3 (1.58%) are ITALY 42 | - 1 (0.53%) are CZECH REPUBLIC 43 | - 0 (0.0%) are DENMARK 44 | - 6 (3.16%) are CYPRUS 45 | - 0 (0.0%) have no Country value 46 | 47 | *Preview Analysis* (No files written): 48 | 16 clusters in data set 1 (22.54%) have more than 2 sequences that match between data sets. 49 | Of these, 12 clusters (16.9%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 1 50 | Of the 46 sequences in the clusters returned from data set 1: 51 | - 0 (0.0%) are SPAIN 52 | - 0 (0.0%) are BELGIUM 53 | - 0 (0.0%) are GERMANY 54 | - 0 (0.0%) are FRANCE 55 | - 43 (93.48%) are UNITED KINGDOM 56 | - 0 (0.0%) are GREECE 57 | - 3 (6.52%) are ITALY 58 | - 0 (0.0%) are CZECH REPUBLIC 59 | - 0 (0.0%) are DENMARK 60 | - 0 (0.0%) are CYPRUS 61 | - 0 (0.0%) have no Country value 62 | Of the 99 sequences in the matching clusters returned from data set 2: 63 | - 0 (0.0%) are SPAIN 64 | - 0 (0.0%) are BELGIUM 65 | - 0 (0.0%) are GERMANY 66 | - 0 (0.0%) are FRANCE 67 | - 92 (92.93%) are UNITED KINGDOM 68 | - 0 (0.0%) are GREECE 69 | - 3 (3.03%) are ITALY 70 | - 0 (0.0%) are CZECH REPUBLIC 71 | - 0 (0.0%) are DENMARK 72 | - 4 (4.04%) are CYPRUS 73 | - 0 (0.0%) have no Country value 74 | 75 | *Preview Analysis* (No files written): 76 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 77 | Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2 78 | 79 | *Preview Analysis* (No files written): 80 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 81 | Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2 82 | 83 | *FigTree Files Written*: 84 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles 85 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 86 | Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2 87 | 88 | **Previously Written Files Were Deleted!** 89 | 90 | *FigTree Files Written*: 91 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles 92 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 93 | Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in both data sets 94 | Of the 103 sequences in the clusters returned from data set 1: 95 | - 0 (0.0%) are SPAIN 96 | - 2 (1.94%) are BELGIUM 97 | - 0 (0.0%) are GERMANY 98 | - 0 (0.0%) are FRANCE 99 | - 97 (94.17%) are UNITED KINGDOM 100 | - 0 (0.0%) are GREECE 101 | - 3 (2.91%) are ITALY 102 | - 1 (0.97%) are CZECH REPUBLIC 103 | - 0 (0.0%) are DENMARK 104 | - 0 (0.0%) are CYPRUS 105 | - 0 (0.0%) have no Country value 106 | Of the 190 sequences in the matching clusters returned from data set 2: 107 | - 0 (0.0%) are SPAIN 108 | - 2 (1.05%) are BELGIUM 109 | - 0 (0.0%) are GERMANY 110 | - 0 (0.0%) are FRANCE 111 | - 178 (93.68%) are UNITED KINGDOM 112 | - 0 (0.0%) are GREECE 113 | - 3 (1.58%) are ITALY 114 | - 1 (0.53%) are CZECH REPUBLIC 115 | - 0 (0.0%) are DENMARK 116 | - 6 (3.16%) are CYPRUS 117 | - 0 (0.0%) have no Country value 118 | 119 | **Previously Written Files Were Deleted!** 120 | 121 | *FigTree Files Written*: 122 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles 123 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 124 | Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in both data sets 125 | Of the 103 sequences in the clusters returned from data set 1: 126 | - 0 (0.0%) are SPAIN 127 | - 2 (1.94%) are BELGIUM 128 | - 0 (0.0%) are GERMANY 129 | - 0 (0.0%) are FRANCE 130 | - 97 (94.17%) are UNITED KINGDOM 131 | - 0 (0.0%) are GREECE 132 | - 3 (2.91%) are ITALY 133 | - 1 (0.97%) are CZECH REPUBLIC 134 | - 0 (0.0%) are DENMARK 135 | - 0 (0.0%) are CYPRUS 136 | - 0 (0.0%) have no Country value 137 | Of the 190 sequences in the matching clusters returned from data set 2: 138 | - 0 (0.0%) are SPAIN 139 | - 2 (1.05%) are BELGIUM 140 | - 0 (0.0%) are GERMANY 141 | - 0 (0.0%) are FRANCE 142 | - 178 (93.68%) are UNITED KINGDOM 143 | - 0 (0.0%) are GREECE 144 | - 3 (1.58%) are ITALY 145 | - 1 (0.53%) are CZECH REPUBLIC 146 | - 0 (0.0%) are DENMARK 147 | - 6 (3.16%) are CYPRUS 148 | - 0 (0.0%) have no Country value 149 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU1866/EU1866.treeforCPT_clusterPicks_log.txt: -------------------------------------------------------------------------------- 1 | ** Cluster Picker Results ** 2 | Input sequences = C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.fas 3 | Input tree = C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.treeforCPT.nwk 4 | Initial support threshold= 0.9 5 | Support threshold= 0.9 6 | Genetic distance threshold= 0.045 7 | Large cluster threshold= 5 8 | ------------------------- 9 | ** Sequences with cluster assignment output with new names 10 | ** Tree modified to contain new names 11 | ** new names have form: Clust(C)_(SequenceName) where C = cluster number, e.g. Clust25_139320 12 | ------------------------- 13 | Output sequences = C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866_EU1866.treeforCPT_clusterPicks.fas 14 | Output tree= C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.treeforCPT_clusterPicks.nwk 15 | Output figtree= C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.treeforCPT_clusterPicks.nwk.figTree 16 | ------------------------- 17 | There are 1866 sequences 18 | Tree has 1866 tips 19 | Found 71 clusters 20 | ClusterNumber NumberOfTips NumberOfTipsCheck TipNames Bootstrap GD 21 | 1 2 2 [B.GB.1182_48_8095_20030909.DQ879092_2003, B.GB.80597.JN101915_1998] 0.998 0.01901901901901902 22 | 2 2 2 [B.CZ.82729PL1.AY694293_2000, B.CZ.86543PL1.AY694321_2001] 1.0 0.013013013013013013 23 | 3 2 2 [B.GB.67444.JN101626_1999, B.GB.73199.JN101836_2002] 1.0 0.015015015015015015 24 | 4 2 2 [B.GB.78956.JN100840_1998, B.GB.93301.JN101878_2002] 0.926 0.03003003003003003 25 | 5 2 2 [B.GB.72086.JN100900_2001, B.GB.74246.JN100899_1997] 0.984 0.04104104104104104 26 | 6 2 2 [B.GB.77754.JN101198_1999, B.GB.79261.JN100976_2003] 1.0 0.02002002002002002 27 | 7 2 2 [B.GB.81423.JN100924_2002, B.GB.99418.JN100857_2003] 0.973 0.03403403403403404 28 | 8 2 2 [B.BE.VI2681.DQ177234_2002, B.GB.94777.JN101269_1998] 0.975 0.035035035035035036 29 | 9 3 3 [B.GB.98050.JN101673_2003, B.GB.79862.JN101284_2001, B.GB.67817.JN100938_2000] 0.917 0.043043043043043044 30 | 10 2 2 [B.BE.Q34.DQ061392_1997, B.IT.56MUS.EU496236_2001] 0.904 0.026026026026026026 31 | 11 3 3 [B.GB.90699.JN101771_2003, B.GB.77726.JN101793_2002, B.GB.81527.JN101079_2003] 1.0 0.025025025025025027 32 | 12 5 5 [B.CZ.74936PL9.AY694378_2000, B.CZ.SL10243PL10.AY694335_2000, B.CZ.87914PL1.AY694382_2000, B.CZ.83862PL1.AY694278_2000, B.CZ.85459PL1.AY694271_2000] 0.993 0.03003003003003003 33 | 13 2 2 [B.GB.86642.JN101637_2002, B.GB.92422.JN101343_2001] 0.902 0.03903903903903904 34 | 14 2 2 [B.GB.80473.JN100941_1999, B.GB.86548.JN101591_1997] 0.953 0.02902902902902903 35 | 15 2 2 [B.GB.67364.JN100826_2003, B.GB.98778.JN100725_1997] 0.997 0.015015015015015015 36 | 16 2 2 [B.GB.81432.JN101725_2000, B.GB.93296.JN101060_2001] 0.919 0.035035035035035036 37 | 17 2 2 [B.GB.75429.JN100795_2002, B.GB.96540.JN101434_2001] 0.93 0.035035035035035036 38 | 18 2 2 [B.GB.89250.JN100855_2000, B.GB.99800.JN101479_1997] 0.99 0.024024024024024024 39 | 19 3 3 [B.CZ.85600PL1.AY694273_2000, B.CZ.85522PL1.AY694281_2000, B.CZ.85534PL1.AY694272_2000] 1.0 0.002002002002002002 40 | 20 2 2 [B.GB.117850.AY362171_1999, B.GB.GB8_46R.AJ271445_1986] 0.907 0.04104104104104104 41 | 21 2 2 [B.GB.73675.JN101181_2001, B.GB.85208.JN101510_1997] 0.993 0.04104104104104104 42 | 22 2 2 [B.GB.89544.JN100806_2002, B.GB.99354.JN101168_2003] 1.0 0.006006006006006006 43 | 23 2 2 [B.GB.78634.JN101739_2002, B.GB.93560.JN101070_2003] 0.964 0.01901901901901902 44 | 24 2 2 [B.GB.84844.JN101826_2000, B.GB.99561.JN100810_2002] 1.0 0.014014014014014014 45 | 25 2 2 [B.BE.VI2626.DQ177220_2002, B.GB.78944.JN100785_2001] 0.965 0.036036036036036036 46 | 26 3 3 [B.GB.67617.JN101251_2003, B.GB.77502.JN101714_2003, B.GB.85525.JN101202_2003] 1.0 0.03203203203203203 47 | 27 2 2 [B.CZ.70948PL16.AY694250_2000, B.CZ.82516PL1.AY694288_2000] 0.938 0.044044044044044044 48 | 28 2 2 [B.GB.84710.JN100911_2000, B.GB.97425.JN100776_2003] 1.0 0.021021021021021023 49 | 29 3 3 [B.IT.58MUS.EU496238_2001, B.GB.66582.JN101213_1998, B.GB.81580.JN101293_1998] 0.994 0.035035035035035036 50 | 30 2 2 [B.GB.71430.JN101115_1997, B.GB.81920.JN101219_2002] 0.98 0.04104104104104104 51 | 31 5 5 [B.GB.77801.JN101755_2001, B.GB.91436.JN101406_1998, B.GB.92656.JN101265_1999, B.IT.1182_48_6231_20030930.DQ878798_2003, B.IT.65MUS.EU496245_2001] 0.903 0.044044044044044044 52 | 32 6 6 [B.GB.clA_s7_n_y03.EU817066_2003, B.GB.clA_s11_n_y98.EU817049_1998, B.GB.clA_s19_n_y03.EU817057_2003, B.GB.clA_s3_n_y01.EU817062_2001, B.GB.clA_s12_n_y03.EU817050_2003, B.GB.clA_s20_n_y01.EU817059_2001] 1.0 0.023023023023023025 53 | 33 2 2 [B.BE.VI2687.DQ177228_2002, B.BE.VI339.DQ177224_1989] 0.901 0.028028028028028028 54 | 34 2 2 [B.GB.78918.JN100676_1997, B.GB.88379.JN101511_2002] 1.0 0.02002002002002002 55 | 35 2 2 [B.DE.1182_48_4238_20030513.DQ878469_2003, B.DE.1182_48_4240_20030513.DQ878471_2003] 0.999 0.005005005005005005 56 | 36 2 2 [B.FR.1182_48_3262_20030729.DQ878166_2003, B.FR.1182_48_3297_20030930.DQ878203_2003] 1.0 0.022022022022022022 57 | 37 2 2 [B.GR.1182_48_5097_20030901.DQ878593_2003, B.GR.1182_48_5098_20030925.DQ878594_2003] 0.964 0.04004004004004004 58 | 38 2 2 [B.DE.1182_48_4215_20030512.DQ878448_2003, B.DE.ID1083_GT2.GU271161_2002] 0.998 0.012012012012012012 59 | 39 2 2 [B.DE.1182_48_4137_20030320.DQ878368_2003, B.DE.1182_48_4176_20030506.DQ878410_2003] 0.998 0.03403403403403404 60 | 40 6 6 [B.GB.67840.JN101388_2000, B.GB.clB_s34_n_y03.EU817080_2003, B.GB.94935.JN100995_2003, B.GB.clB_s26_n_y02.EU817072_2002, B.GB.clB_s35_n_y01.EU817081_2001, B.GB.clB_s33_n_y00.EU817079_2000] 1.0 0.015015015015015015 61 | 41 2 2 [B.CZ.83315PL1.AY694284_2000, B.CZ.80110PL7.AY694323_2001] 0.992 0.028028028028028028 62 | 42 3 3 [B.GB.68766.JN100981_2003, B.GB.89288.JN101121_2003, B.GB.97209.JN101418_2003] 0.967 0.036036036036036036 63 | 43 5 5 [B.GB.76091.JN101249_2003, B.GB.66215.JN100858_2003, B.GB.80439.JN101149_2003, B.GB.84479.JN101925_2003, B.GB.83164.JN101313_2002] 0.978 0.035035035035035036 64 | 44 3 3 [B.GB.98979.JN100701_2000, B.GB.66386.JN100703_2002, B.GB.92457.JN101143_2003] 0.962 0.03403403403403404 65 | 45 2 2 [B.CZ.87053PL1.AY694344_2000, B.GB.87781.JN101429_2001] 1.0 0.014014014014014014 66 | 46 2 2 [B.GB.79271.JN101525_2002, B.GB.79911.JN101167_1999] 0.98 0.03803803803803804 67 | 47 2 2 [B.CZ.87933PL1.AY694377_2000, B.CZ.SL15556PL1.AY694295_2000] 0.988 0.042042042042042045 68 | 48 2 2 [B.GB.71435.JN101658_2001, B.GB.95500.JN100856_2002] 1.0 0.011011011011011011 69 | 49 2 2 [B.GB.84724.JN101059_2000, B.GB.91777.JN101452_2001] 1.0 0.008008008008008008 70 | 50 3 3 [B.CZ.87009PL1.AY694339_2000, B.CZ.84453PL2.AY694265_2000, B.CZ.84878PL1.AY694276_2000] 0.985 0.023023023023023025 71 | 51 2 2 [B.BE.M24.DQ061388_1996, B.GB.96768.JN100825_1999] 0.926 0.031031031031031032 72 | 52 2 2 [B.IT.36MUS.EU496216_2001, B.IT.39MUS.EU496219_2001] 0.904 0.043043043043043044 73 | 53 2 2 [B.GB.1182_48_8009_20030506.DQ879054_2003, B.GB.71670.JN101435_2002] 0.975 0.037037037037037035 74 | 54 2 2 [B.CZ.85755PL1.AY694301_2000, B.DE.1182_48_4122_20030409.DQ878353_2003] 0.999 0.026026026026026026 75 | 55 2 2 [B.GB.100346.JN100671_2002, B.GB.70066.JN101924_2003] 0.998 0.02702702702702703 76 | 56 2 2 [B.CZ.52540PL14.AY694308_2000, B.CZ.79664PL1.AY694292_2000] 1.0 0.018018018018018018 77 | 57 2 2 [B.ES.1182_48_7098_20030714.DQ878951_2003, B.ES.2_1_99.AY188569_1999] 0.999 0.03803803803803804 78 | 58 2 2 [B.FR.1182_48_3149_20030429.DQ878060_2003, B.FR.1182_48_3258_20030812.DQ878162_2003] 1.0 0.031031031031031032 79 | 59 2 2 [B.FR.1182_48_3195_20030512.DQ878105_2003, B.FR.1182_48_3212_20030731.DQ878122_2003] 1.0 0.01001001001001001 80 | 60 2 2 [B.DE.1182_48_4002_20030311.DQ878235_2003, B.DE.1182_48_4174_20030502.DQ878408_2003] 1.0 0.012012012012012012 81 | 61 2 2 [B.DE.1182_48_4054_20030430.DQ878286_2003, B.DE.1182_48_4231_20030618.DQ878463_2003] 1.0 0.006006006006006006 82 | 62 2 2 [B.FR.1182_48_3169_20030409.DQ878078_2003, B.FR.1182_48_3303_20030911.DQ878207_2003] 1.0 0.003003003003003003 83 | 63 2 2 [B.DE.1182_48_4261_20030530.DQ878493_2003, B.DE.ID1561_GT2.GU271167_2002] 0.996 0.015015015015015015 84 | 64 3 3 [B.GB.75704.JN101005_2002, B.GB.82650.JN101373_2000, B.GB.98537.JN101671_2003] 1.0 0.009009009009009009 85 | 65 3 3 [B.DE.1182_48_4109_20030304.DQ878339_2003, B.DE.1182_48_4050_20030218.DQ878283_2003, B.DE.1182_48_4110_20030311.DQ878340_2003] 0.995 0.04004004004004004 86 | 66 2 2 [B.GB.91351.JN100798_2000, B.GB.98260.JN101870_2001] 0.92 0.03403403403403404 87 | 67 2 2 [B.GB.87761.JN101601_2003, B.GB.MM33d391_P4.HM586190_2001] 0.998 0.014014014014014014 88 | 68 3 3 [B.GB.A295.AF494112_1995, B.GB.B4-bp1.AF494110_1998, B.GB.C198.AF494111_1998] 0.943 0.03903903903903904 89 | 69 2 2 [B.GB.77183.JN101935_2003, B.GB.80117.JN101943_2003] 0.999 0.016016016016016016 90 | 70 3 3 [B.GB.76784.JN101000_2000, B.GB.87532.JN101089_2003, B.GB.90653.JN101465_2003] 0.997 0.021021021021021023 91 | 71 2 2 [B.GB.71329.JN101640_2000, B.GB.93775.JN101884_2003] 0.982 0.031031031031031032 92 | ------------------------- 93 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster12_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.CZ.74936PL9.AY694378_2000 2 | B.CZ.SL10243PL10.AY694335_2000 3 | B.CZ.87914PL1.AY694382_2000 4 | B.CZ.83862PL1.AY694278_2000 5 | B.CZ.85459PL1.AY694271_2000 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster31_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.77801.JN101755_2001 2 | B.GB.91436.JN101406_1998 3 | B.GB.92656.JN101265_1999 4 | B.IT.1182_48_6231_20030930.DQ878798_2003 5 | B.IT.65MUS.EU496245_2001 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster32_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.clA_s7_n_y03.EU817066_2003 2 | B.GB.clA_s11_n_y98.EU817049_1998 3 | B.GB.clA_s19_n_y03.EU817057_2003 4 | B.GB.clA_s3_n_y01.EU817062_2001 5 | B.GB.clA_s12_n_y03.EU817050_2003 6 | B.GB.clA_s20_n_y01.EU817059_2001 7 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster40_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.67840.JN101388_2000 2 | B.GB.clB_s34_n_y03.EU817080_2003 3 | B.GB.94935.JN100995_2003 4 | B.GB.clB_s26_n_y02.EU817072_2002 5 | B.GB.clB_s35_n_y01.EU817081_2001 6 | B.GB.clB_s33_n_y00.EU817079_2000 7 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster43_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.76091.JN101249_2003 2 | B.GB.66215.JN100858_2003 3 | B.GB.80439.JN101149_2003 4 | B.GB.84479.JN101925_2003 5 | B.GB.83164.JN101313_2002 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster101_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.77420.JN101554_2006 2 | B.GB.68766.JN100981_2003 3 | B.GB.97209.JN101418_2003 4 | B.GB.70144.JN101096_2006 5 | B.GB.89288.JN101121_2003 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster121_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.IT.1182_48_6231_20030930.DQ878798_2003 2 | B.IT.65MUS.EU496245_2001 3 | B.GB.77801.JN101755_2001 4 | B.GB.91436.JN101406_1998 5 | B.GB.92656.JN101265_1999 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster124_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.CY.CY267.JF683808_2009 2 | B.CY.CY216.JF683765_2007 3 | B.CY.CY246.JF683791_2009 4 | B.GB.clA_s7_n_y03.EU817066_2003 5 | B.GB.100222.JN100794_2006 6 | B.GB.clA_s19_n_y03.EU817057_2003 7 | B.GB.clA_s5_n_y05.EU817064_2005 8 | B.GB.clA_s3_n_y01.EU817062_2001 9 | B.GB.clA_s8_n_y04.EU817067_2004 10 | B.GB.clA_s4_n_y05.EU817063_2005 11 | B.GB.clA_s11_n_y98.EU817049_1998 12 | B.GB.clA_s12_n_y03.EU817050_2003 13 | B.GB.clA_s22_n_y04.EU817061_2004 14 | B.GB.clA_s10_n_y04.EU817048_2004 15 | B.GB.clA_s21_n_y05.EU817060_2005 16 | B.GB.clA_s18_n_y05.EU817056_2005 17 | B.GB.clA_s1_n_y05.EU817047_2005 18 | B.GB.clA_s13_n_y05.EU817051_2005 19 | B.GB.clA_s9_n_y05.EU817068_2005 20 | B.GB.clA_s17_n_y05.EU817055_2005 21 | B.GB.clA_s6_n_y05.EU817065_2005 22 | B.GB.clA_s14_n_y05.EU817052_2005 23 | B.GB.clA_s16_n_y04.EU817054_2004 24 | B.GB.clA_s2_n_y05.EU817058_2005 25 | B.GB.clA_s20_n_y01.EU817059_2001 26 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster138_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.67617.JN101251_2003 2 | B.GB.85525.JN101202_2003 3 | B.CY.CY188.JF683741_2007 4 | B.GB.77502.JN101714_2003 5 | B.GB.79655.JN100780_2004 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster170_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.93560.JN101070_2003 2 | B.GB.87483.JN101890_2006 3 | B.GB.66276.JN101792_2004 4 | B.GB.90983.JN101486_2007 5 | B.GB.92247.JN101686_2004 6 | B.GB.67944.JN101323_2005 7 | B.GB.78634.JN101739_2002 8 | B.GB.95495.JN101896_2006 9 | B.GB.75888.JN101084_2005 10 | B.GB.100389.JN101100_2005 11 | B.GB.77565.JN101663_2005 12 | B.GB.94134.JN101081_2006 13 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster171_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.85374.JN100797_2007 2 | B.GB.86273.JN101404_2004 3 | B.CZ.85600PL1.AY694273_2000 4 | B.CZ.85522PL1.AY694281_2000 5 | B.CZ.85534PL1.AY694272_2000 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster178_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.BE.VI2626.DQ177220_2002 2 | B.GB.78944.JN100785_2001 3 | B.GB.74215.JN101676_2005 4 | B.GB.98658.JN101551_2005 5 | B.GB.80074.JN101810_2006 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster195_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.89578.JN101677_2006 2 | B.GB.clB_s30_n_y05.EU817076_2005 3 | B.GB.67840.JN101388_2000 4 | B.GB.clB_s34_n_y03.EU817080_2003 5 | B.GB.89742.JN101197_2004 6 | B.GB.clB_s32_n_y04.EU817078_2004 7 | B.GB.67620.JN101107_2004 8 | B.GB.clB_s27_n_y05.EU817073_2005 9 | B.GB.clB_s29_n_y04.EU817075_2004 10 | B.GB.clB_s23_e_y05.EU817069_2005 11 | B.GB.92595.JN101090_2006 12 | B.GB.clB_s24_n_y05.EU817070_2005 13 | B.GB.clB_s31_n_y05.EU817077_2005 14 | B.GB.clB_s26_n_y02.EU817072_2002 15 | B.GB.94935.JN100995_2003 16 | B.GB.clB_s35_n_y01.EU817081_2001 17 | B.GB.clB_s33_n_y00.EU817079_2000 18 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster196_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.94194.JN101436_2005 2 | B.GB.90699.JN101771_2003 3 | B.GB.97927.JN101459_2006 4 | B.GB.81527.JN101079_2003 5 | B.GB.84709.JN100948_2005 6 | B.GB.90776.JN101207_2005 7 | B.GB.77726.JN101793_2002 8 | B.GB.92178.JN101881_2005 9 | B.GB.77900.JN101895_2005 10 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster202_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.75704.JN101005_2002 2 | B.GB.82699.JN100737_2006 3 | B.GB.82650.JN101373_2000 4 | B.GB.67479.JN101053_2004 5 | B.GB.98537.JN101671_2003 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster210_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.IT.CV1136_102_07.GU969514_2007 2 | B.IT.CV1170_34_08.GU969535_2008 3 | B.IT.CV1068_133_06.GU969486_2006 4 | B.IT.CV1054_124_06.GU969484_2006 5 | B.IT.CV984_73_06.GU969495_2006 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster222_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.87022.JN100991_2006 2 | B.GB.85037.JN101741_2006 3 | B.GB.95401.JN101931_2006 4 | B.GB.91315.JN101880_2006 5 | B.GB.99939.JN101230_2006 6 | B.GB.66778.JN101390_2007 7 | B.GB.74719.JN101482_2006 8 | B.GB.96102.JN101903_2006 9 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster224_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.71102.JN101174_2007 2 | B.GB.100346.JN100671_2002 3 | B.CY.CY032.FJ388898_2005 4 | B.GB.68367.JN100665_2005 5 | B.GB.70066.JN101924_2003 6 | B.GB.79058.JN101649_2004 7 | B.GB.67719.JN100903_2005 8 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster30_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.CZ.74936PL9.AY694378_2000 2 | B.CZ.SL10243PL10.AY694335_2000 3 | B.CZ.87914PL1.AY694382_2000 4 | B.CZ.83862PL1.AY694278_2000 5 | B.CZ.85459PL1.AY694271_2000 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster33_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.ES.05SP0243938.FJ481768_2005 2 | B.GB.clC_s36_n_y02.EU817085_2002 3 | B.GB.clC_s37_n_y05.EU817083_2005 4 | B.GB.clC_s38_n_y05.EU817084_2005 5 | B.GB.clC_s39_n_y05.EU817082_2005 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster52_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.ES.06SP375981.FJ481724_2004 2 | B.GB.78259.JN101664_2006 3 | B.GB.73798.JN101733_2006 4 | B.GB.66323.JN101240_2006 5 | B.GB.74805.JN100993_2006 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster59_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.78819.JN101134_2006 2 | B.GB.67806.JN101768_2006 3 | B.GB.85950.JN100949_2006 4 | B.GB.67690.JN101153_2005 5 | B.GB.80753.JN101565_2006 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster67_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.99681.JN101492_2005 2 | B.GB.73733.JN100702_2004 3 | B.GB.76784.JN101000_2000 4 | B.GB.88278.JN101928_2005 5 | B.GB.87532.JN101089_2003 6 | B.GB.90653.JN101465_2003 7 | B.GB.100215.JN101585_2006 8 | B.GB.91074.JN101860_2006 9 | B.GB.70017.JN101347_2005 10 | B.GB.75726.JN100864_2004 11 | B.GB.89166.JN100726_2005 12 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster76_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.90600.JN101941_2005 2 | B.GB.98979.JN100701_2000 3 | B.GB.71304.JN101646_2004 4 | B.GB.66386.JN100703_2002 5 | B.GB.92457.JN101143_2003 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster78_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.98843.JN101324_1998 2 | B.GB.79202.JN101094_2006 3 | B.GB.76818.JN101805_2005 4 | B.GB.84248.JN101879_2006 5 | B.GB.66208.JN101066_2006 6 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster86_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.71034.JN101542_2006 2 | B.GB.80026.JN100890_2006 3 | B.GB.92351.JN101666_2005 4 | B.CZ.87053PL1.AY694344_2000 5 | B.GB.87781.JN101429_2001 6 | B.GB.85080.JN101871_2006 7 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster90_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.83454.JN100715_2007 2 | B.GB.80556.JN100690_2004 3 | B.GB.81851.JN101058_2005 4 | B.GB.72891.JN101607_2005 5 | B.GB.95835.JN100677_2006 6 | B.GB.88392.JN101780_2006 7 | B.GB.96861.JN101534_2006 8 | B.GB.92932.JN101904_2005 9 | B.ES.X2510_1.GU326114_2008 10 | -------------------------------------------------------------------------------- /Tutorial/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster95_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.71413.JN101645_2004 2 | B.GB.80439.JN101149_2003 3 | B.GB.84479.JN101925_2003 4 | B.GB.91251.JN101907_2006 5 | B.GB.66215.JN100858_2003 6 | -------------------------------------------------------------------------------- /Tutorial/Tutorial_January2016.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/Tutorial/Tutorial_January2016.pdf -------------------------------------------------------------------------------- /Tutorial/combine_CPCM.R: -------------------------------------------------------------------------------- 1 | ### combine CP/CM output 2 | ### M. Ragonnet 3 | ### 5th Feb 2014 4 | 5 | ## CM is cluster matcher 6 | ## CP is cluster picker 7 | ## the files output from each program should be in the same folder 8 | 9 | setwd("") 10 | path <- getwd() 11 | print(path) 12 | 13 | ## read the files 14 | #read the cm file 15 | txtFolder <- dir(path) 16 | inds <- grep("clustInfo", txtFolder) 17 | clustInfoFile <- txtFolder[inds] 18 | cm <- read.csv(clustInfoFile, header=TRUE) 19 | 20 | #read the CP log file 21 | cp_output <- readLines(list.files(pattern="*clusterPicks_log.txt")) 22 | cp_output2 <- cp_output[20:(length(cp_output)-1)] 23 | writeLines(cp_output2, "CP_output.txt") 24 | cp <- read.table("CP_output.txt", sep="\t", header=TRUE) 25 | colnames(cp)[1] <- "Clust_ID" 26 | 27 | # merge the files into one superfile and write to folder 28 | cluster_table <- merge(cp,cm,by=c("Clust_ID"), all=TRUE) 29 | 30 | 31 | for (line in 1:length(cluster_table[,1])){ 32 | if(cluster_table$NumberOfTips [line] != cluster_table$Num_Seqs[line]){ 33 | print("There was a problem combining the files!") 34 | } 35 | } 36 | 37 | write.csv (cluster_table, file ="cpcm.csv", row.names = FALSE) 38 | -------------------------------------------------------------------------------- /Tutorial/launchCPloop.py: -------------------------------------------------------------------------------- 1 | # This script launches CP on a series of nwk trees 2 | # Remember bootstraps are out of 100 for Raxml and out of 1 for FastTree!!! 3 | # M. Ragonnet 4 | # 21st June 2013 5 | 6 | import subprocess as sub 7 | import os 8 | 9 | # to launch on 100 simulated sequences and trees in the same folder 10 | 11 | for i in range(1,101): 12 | sub.call(["java", "-jar", "ClusterPicker_1.2.jar", 13 | "tree"+str(i)+"_simulatedSeqs.fas", "tree"+str(i)+".nwk", "90", "90","0.045","0"]) 14 | 15 | 16 | # to launch in folders and subfolders with structure bootstrap --> genetic distance 17 | 18 | bootstraps = [0.70,0.80,0.90, 0.95] 19 | genetic_distances =[0.015, 0.045] 20 | root = os.getcwd() 21 | 22 | for j in range(len(genetic_distances)): 23 | for i in range(len(bootstraps)): 24 | print(os.getcwd()) 25 | os.chdir(root+ "/"+str(bootstraps[i])+"/"+str(genetic_distances[j])) 26 | print (bootstraps[i]) 27 | sub.call(["java", "-jar", "ClusterPicker_1.2.jar", "fastaFile.fas", 28 | "tree.nwk", str(bootstraps[i]), str(bootstraps[i]),str(genetic_distances[j]),"0", "ambiguity"]) 29 | 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Ragonnet 3 | ### 5th Feb 2014 4 | 5 | ## CM is cluster matcher 6 | ## CP is cluster picker 7 | ## the files output from each program should be in the same folder 8 | 9 | setwd("") 10 | path <- getwd() 11 | print(path) 12 | 13 | ## read the files 14 | #read the cm file 15 | txtFolder <- dir(path) 16 | inds <- grep("clustInfo", txtFolder) 17 | clustInfoFile <- txtFolder[inds] 18 | cm <- read.csv(clustInfoFile, header=TRUE) 19 | 20 | #read the CP log file 21 | cp_output <- readLines(list.files(pattern="*clusterPicks_log.txt")) 22 | cp_output2 <- cp_output[20:(length(cp_output)-1)] 23 | writeLines(cp_output2, "CP_output.txt") 24 | cp <- read.table("CP_output.txt", sep="\t", header=TRUE) 25 | colnames(cp)[1] <- "Clust_ID" 26 | 27 | # merge the files into one superfile and write to folder 28 | cluster_table <- merge(cp,cm,by=c("Clust_ID"), all=TRUE) 29 | 30 | 31 | for (line in 1:length(cluster_table[,1])){ 32 | if(cluster_table$NumberOfTips [line] != cluster_table$Num_Seqs[line]){ 33 | print("There was a problem combining the files!") 34 | } 35 | } 36 | 37 | write.csv (cluster_table, file ="cpcm.csv", row.names = FALSE) 38 | -------------------------------------------------------------------------------- /docs/ClusterMatcher_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/docs/ClusterMatcher_manual.pdf -------------------------------------------------------------------------------- /docs/ClusterPicker1.2_Manual_Sept2015.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/docs/ClusterPicker1.2_Manual_Sept2015.pdf -------------------------------------------------------------------------------- /docs/ClusterTutorial/HCV/0.9_2/HCV3876_clusterPicks_log.txt: -------------------------------------------------------------------------------- 1 | ** Cluster Picker Results ** 2 | Input sequences = C:\Users\Manon\Documents\Project\CPT_Write-up\BMCcorrections\HCV\HCV_1b_3876.fas 3 | Input tree = C:\Users\Manon\Documents\Project\CPT_Write-up\BMCcorrections\HCV\HCV3876.nwk 4 | Initial support threshold= 90.0 5 | Support threshold= 90.0 6 | Genetic distance threshold= 0.02 7 | Large cluster threshold= 2147483647 8 | ------------------------- 9 | ** Sequences with cluster assignment output with new names 10 | ** Tree modified to contain new names 11 | ** new names have form: Clust(C)_(SequenceName) where C = cluster number, e.g. Clust25_139320 12 | ------------------------- 13 | Output sequences = C:\Users\Manon\Documents\Project\CPT_Write-up\BMCcorrections\HCV\HCV_1b_3876_HCV3876_clusterPicks.fas 14 | Output tree= C:\Users\Manon\Documents\Project\CPT_Write-up\BMCcorrections\HCV\HCV3876_clusterPicks.nwk 15 | Output figtree= C:\Users\Manon\Documents\Project\CPT_Write-up\BMCcorrections\HCV\HCV3876_clusterPicks.nwk.figTree 16 | ------------------------- 17 | There are 3876 sequences 18 | Tree has 3876 tips 19 | Found 50 clusters 20 | ClusterNumber NumberOfTips NumberOfTipsCheck TipNames Bootstrap GD 21 | 1 7 7 [AY587359, AY587353, AY587357, AY587352, AY587356, AY587354, AY587364] 93.0 0.008726003490401396 22 | 2 2 2 [KC143930, KC143928] 95.0 0.0034904013961605585 23 | 3 2 2 [AY835228, AY835227] 93.0 0.005235602094240838 24 | 4 8 8 [AY587496, AY587482, AY587497, AY587484, AY587486, AY587487, AY587490, AY587483] 95.0 0.013961605584642234 25 | 5 3 3 [AF139594, S62220, D13406] 99.0 0.005235602094240838 26 | 6 2 2 [AB269350, AB291028] 100.0 0.0017452006980802793 27 | 7 2 2 [FJ607132, FJ607113] 98.0 0.005235602094240838 28 | 8 7 7 [AY587420, AY587426, AY587428, AY587415, AY587421, AY587414, AY587419] 91.0 0.006980802792321117 29 | 9 2 2 [DQ374421, AY506680] 96.0 0.0034904013961605585 30 | 10 2 2 [AB719578, AB719498] 99.0 0.0034904013961605585 31 | 11 2 2 [AF165049, AF165050] 96.0 0.005235602094240838 32 | 12 2 2 [FJ483372, FJ607089] 100.0 0.0017452006980802793 33 | 13 12 12 [AY600729, AY600728, AY600733, AY600731, AY600735, AY600736, AY600715, AY600739, AY600738, AY600707, AY600708, AY600737] 91.0 0.010471204188481676 34 | 14 2 2 [FJ911717, FJ911733] 97.0 0.005235602094240838 35 | 15 2 2 [D16751, D16766] 99.0 0.005235602094240838 36 | 16 4 4 [X61596, X61591, X78951, X61594] 90.0 0.017452006980802792 37 | 17 2 2 [AB779562, AB779679] 93.0 0.005235602094240838 38 | 18 2 2 [DQ641968, DQ839199] 96.0 0.0017452006980802793 39 | 19 2 2 [DQ641969, DQ839200] 99.0 0.0017452006980802793 40 | 20 2 2 [DQ641973, DQ839204] 97.0 0.0017452006980802793 41 | 21 14 14 [JN981189, JN981196, JN981207, JN981191, JN981201, JN981193, JN981194, JN981199, JN981200, JN981197, JN981204, JN981188, JN981190, JN981206] 95.0 0.013961605584642234 42 | 22 2 2 [AM262500, AM262494] 91.0 0.0017452006980802793 43 | 23 2 2 [D11355, D11168] 100.0 0.0034904013961605585 44 | 24 2 2 [AY835286, AY835287] 94.0 0.013961605584642234 45 | 25 2 2 [AB518849, AB518858] 95.0 0.0 46 | 26 2 2 [D50484, D50482] 91.0 0.010471204188481676 47 | 27 2 2 [AB154198, AB154197] 99.0 0.0034904013961605585 48 | 28 4 4 [JQ791358, JQ791360, JQ791356, JQ791352] 90.0 0.006980802792321117 49 | 29 3 3 [D16703, D16702, D16704] 91.0 0.006980802792321117 50 | 30 2 2 [EF652687, EF652659] 97.0 0.0034904013961605585 51 | 31 2 2 [AF165061, AF165062] 97.0 0.010471204188481676 52 | 32 3 3 [AB061988, AB061992, AB061989] 91.0 0.0034904013961605585 53 | 33 2 2 [DQ839214, DQ839216] 93.0 0.008726003490401396 54 | 34 2 2 [EF420127, EF420126] 98.0 0.012216404886561954 55 | 35 2 2 [JQ791371, JQ791370] 100.0 0.0017452006980802793 56 | 36 11 11 [JQ791377, JQ791384, JQ791379, JQ791374, JQ791381, JQ791366, JQ791365, JQ791383, JQ791367, JQ791378, JQ791368] 98.0 0.006980802792321117 57 | 37 2 2 [KC143890, KC143884] 93.0 0.0017452006980802793 58 | 38 13 13 [AB492234, AB492230, AB492228, AB492229, AB492235, AB492233, AB492220, AB492221, AB492225, AB492226, AB492219, AB492227, AB492222] 91.0 0.019197207678883072 59 | 39 2 2 [JQ791357, JQ791362] 99.0 0.0017452006980802793 60 | 40 2 2 [JN573006, JN573005] 96.0 0.0017452006980802793 61 | 41 2 2 [D00574, D89815] 97.0 0.006980802792321117 62 | 42 11 11 [AB492209, AB492213, AB492208, AB492210, AB492224, AB492215, AB492214, AB492207, AB492203, AB492204, AB492205] 100.0 0.012216404886561954 63 | 43 2 2 [JQ791349, JQ791345] 94.0 0.0017452006980802793 64 | 44 2 2 [JN981454, JN981450] 90.0 0.0017452006980802793 65 | 45 9 9 [JQ791390, JQ791385, JQ791391, JQ791395, JQ791400, JQ791401, JQ791403, JQ791386, JQ791387] 99.0 0.008726003490401396 66 | 46 2 2 [JQ791396, JQ791388] 93.0 0.0034904013961605585 67 | 47 2 2 [D10687, D10688] 97.0 0.0034904013961605585 68 | 48 8 8 [JN981309, JN981325, JN981316, JN981310, JN981315, JN981319, JN981308, JN981312] 97.0 0.015706806282722512 69 | 49 2 2 [JX649722, JX649718] 93.0 0.006980802792321117 70 | 50 2 2 [JN981481, JN981482] 92.0 0.008726003490401396 71 | ------------------------- 72 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CMoutput/1inputFile/clustInfo_1_20.28.csv: -------------------------------------------------------------------------------- 1 | Clust_ID,Num_Seqs,Madrid,Antwerp,London,BIRMINGHAM,Sampling city_NA,no,yes,Drug naive_NA,SPAIN,BELGIUM,GERMANY,FRANCE,UNITED KINGDOM,GREECE,ITALY,CZECH REPUBLIC,Country_NA,Male Sex with Male,Heterosexual,IV Drug User,Risk factor_NA 2 | 43,5,0,0,0,0,5,3,2,0,0,0,0,0,5,0,0,0,0,4,0,1,0 3 | 40,6,0,0,0,0,6,1,5,0,0,0,0,0,6,0,0,0,0,5,1,0,0 4 | 32,6,0,0,0,0,6,0,6,0,0,0,0,0,6,0,0,0,0,6,0,0,0 5 | 31,5,0,0,0,0,5,4,1,0,0,0,0,0,3,0,2,0,0,5,0,0,0 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CMoutput/1inputFile/log_2012-6-14_20.28.txt: -------------------------------------------------------------------------------- 1 | **Cluster Matcher** 2 | ------------------- 3 | Created 2011 by Emma Hodcroft 4 | Leigh Brown Group, Edinburgh University 5 | ======================================= 6 | 7 | Input files used: 8 | Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU1866\EU1866_clusterPicks.nwk 9 | Annotation file: C:\MyDocuments\Clusters\ClusterTutorial\TestDataset_3031_epiData.csv 10 | Data Set 2: 11 | Newick file: 12 | 13 | The data set had 1866 sequences and 71 clusters (containing 171 sequences (9.16%)) 14 | 15 | 16 | *Preview Analysis* (No files written): 17 | 5 clusters in data set 1 (7.04%) have more than 3 sequences. 18 | 19 | *FigTree Files Written*: 20 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\1inputFile 21 | 5 clusters in data set 1 (7.04%) have more than 3 sequences. 22 | Of these, 4 clusters (5.63%) have at least 1% sequences with a Country value of UNITED KINGDOM 23 | Of the 22 sequences in these clusters: 24 | - 0 (0.0%) are SPAIN 25 | - 0 (0.0%) are BELGIUM 26 | - 0 (0.0%) are GERMANY 27 | - 0 (0.0%) are FRANCE 28 | - 20 (90.91%) are UNITED KINGDOM 29 | - 0 (0.0%) are GREECE 30 | - 2 (9.09%) are ITALY 31 | - 0 (0.0%) are CZECH REPUBLIC 32 | - 0 (0.0%) have no Country value 33 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CMoutput/2inputFiles/log_2012-6-14_20.38.txt: -------------------------------------------------------------------------------- 1 | **Cluster Matcher** 2 | ------------------- 3 | Created 2011 by Emma Hodcroft 4 | Leigh Brown Group, Edinburgh University 5 | ======================================= 6 | 7 | Input files used: 8 | Data Set 1: 9 | Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU1866\EU1866_clusterPicks.nwk 10 | Annotation file: Will not be used (see '?' below) 11 | Data Set 2: 12 | Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU3031\EU3031_clusterPicks.nwk 13 | Annotation file: C:\MyDocuments\Clusters\ClusterTutorial\TestDataset_3031_epiData.csv 14 | 15 | Data set 1 had 1866 sequences and 71 clusters (containing 171 sequences (9.16%)) 16 | Data set 2 had 3031 sequences and 228 clusters (containing 640 sequences (21.12%)) 17 | 18 | 19 | *Preview Analysis* (No files written): 20 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 21 | Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 1 22 | Of the 103 sequences in the clusters returned from data set 1: 23 | - 0 (0.0%) are SPAIN 24 | - 2 (1.94%) are BELGIUM 25 | - 0 (0.0%) are GERMANY 26 | - 0 (0.0%) are FRANCE 27 | - 97 (94.17%) are UNITED KINGDOM 28 | - 0 (0.0%) are GREECE 29 | - 3 (2.91%) are ITALY 30 | - 1 (0.97%) are CZECH REPUBLIC 31 | - 0 (0.0%) are DENMARK 32 | - 0 (0.0%) are CYPRUS 33 | - 0 (0.0%) have no Country value 34 | Of the 190 sequences in the matching clusters returned from data set 2: 35 | - 0 (0.0%) are SPAIN 36 | - 2 (1.05%) are BELGIUM 37 | - 0 (0.0%) are GERMANY 38 | - 0 (0.0%) are FRANCE 39 | - 178 (93.68%) are UNITED KINGDOM 40 | - 0 (0.0%) are GREECE 41 | - 3 (1.58%) are ITALY 42 | - 1 (0.53%) are CZECH REPUBLIC 43 | - 0 (0.0%) are DENMARK 44 | - 6 (3.16%) are CYPRUS 45 | - 0 (0.0%) have no Country value 46 | 47 | *Preview Analysis* (No files written): 48 | 16 clusters in data set 1 (22.54%) have more than 2 sequences that match between data sets. 49 | Of these, 12 clusters (16.9%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 1 50 | Of the 46 sequences in the clusters returned from data set 1: 51 | - 0 (0.0%) are SPAIN 52 | - 0 (0.0%) are BELGIUM 53 | - 0 (0.0%) are GERMANY 54 | - 0 (0.0%) are FRANCE 55 | - 43 (93.48%) are UNITED KINGDOM 56 | - 0 (0.0%) are GREECE 57 | - 3 (6.52%) are ITALY 58 | - 0 (0.0%) are CZECH REPUBLIC 59 | - 0 (0.0%) are DENMARK 60 | - 0 (0.0%) are CYPRUS 61 | - 0 (0.0%) have no Country value 62 | Of the 99 sequences in the matching clusters returned from data set 2: 63 | - 0 (0.0%) are SPAIN 64 | - 0 (0.0%) are BELGIUM 65 | - 0 (0.0%) are GERMANY 66 | - 0 (0.0%) are FRANCE 67 | - 92 (92.93%) are UNITED KINGDOM 68 | - 0 (0.0%) are GREECE 69 | - 3 (3.03%) are ITALY 70 | - 0 (0.0%) are CZECH REPUBLIC 71 | - 0 (0.0%) are DENMARK 72 | - 4 (4.04%) are CYPRUS 73 | - 0 (0.0%) have no Country value 74 | 75 | *Preview Analysis* (No files written): 76 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 77 | Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2 78 | 79 | *Preview Analysis* (No files written): 80 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 81 | Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2 82 | 83 | *FigTree Files Written*: 84 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles 85 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 86 | Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2 87 | 88 | **Previously Written Files Were Deleted!** 89 | 90 | *FigTree Files Written*: 91 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles 92 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 93 | Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in both data sets 94 | Of the 103 sequences in the clusters returned from data set 1: 95 | - 0 (0.0%) are SPAIN 96 | - 2 (1.94%) are BELGIUM 97 | - 0 (0.0%) are GERMANY 98 | - 0 (0.0%) are FRANCE 99 | - 97 (94.17%) are UNITED KINGDOM 100 | - 0 (0.0%) are GREECE 101 | - 3 (2.91%) are ITALY 102 | - 1 (0.97%) are CZECH REPUBLIC 103 | - 0 (0.0%) are DENMARK 104 | - 0 (0.0%) are CYPRUS 105 | - 0 (0.0%) have no Country value 106 | Of the 190 sequences in the matching clusters returned from data set 2: 107 | - 0 (0.0%) are SPAIN 108 | - 2 (1.05%) are BELGIUM 109 | - 0 (0.0%) are GERMANY 110 | - 0 (0.0%) are FRANCE 111 | - 178 (93.68%) are UNITED KINGDOM 112 | - 0 (0.0%) are GREECE 113 | - 3 (1.58%) are ITALY 114 | - 1 (0.53%) are CZECH REPUBLIC 115 | - 0 (0.0%) are DENMARK 116 | - 6 (3.16%) are CYPRUS 117 | - 0 (0.0%) have no Country value 118 | 119 | **Previously Written Files Were Deleted!** 120 | 121 | *FigTree Files Written*: 122 | Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles 123 | 60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets. 124 | Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in both data sets 125 | Of the 103 sequences in the clusters returned from data set 1: 126 | - 0 (0.0%) are SPAIN 127 | - 2 (1.94%) are BELGIUM 128 | - 0 (0.0%) are GERMANY 129 | - 0 (0.0%) are FRANCE 130 | - 97 (94.17%) are UNITED KINGDOM 131 | - 0 (0.0%) are GREECE 132 | - 3 (2.91%) are ITALY 133 | - 1 (0.97%) are CZECH REPUBLIC 134 | - 0 (0.0%) are DENMARK 135 | - 0 (0.0%) are CYPRUS 136 | - 0 (0.0%) have no Country value 137 | Of the 190 sequences in the matching clusters returned from data set 2: 138 | - 0 (0.0%) are SPAIN 139 | - 2 (1.05%) are BELGIUM 140 | - 0 (0.0%) are GERMANY 141 | - 0 (0.0%) are FRANCE 142 | - 178 (93.68%) are UNITED KINGDOM 143 | - 0 (0.0%) are GREECE 144 | - 3 (1.58%) are ITALY 145 | - 1 (0.53%) are CZECH REPUBLIC 146 | - 0 (0.0%) are DENMARK 147 | - 6 (3.16%) are CYPRUS 148 | - 0 (0.0%) have no Country value 149 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU1866/EU1866.treeforCPT_clusterPicks_log.txt: -------------------------------------------------------------------------------- 1 | ** Cluster Picker Results ** 2 | Input sequences = C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.fas 3 | Input tree = C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.treeforCPT.nwk 4 | Initial support threshold= 0.9 5 | Support threshold= 0.9 6 | Genetic distance threshold= 0.045 7 | Large cluster threshold= 5 8 | ------------------------- 9 | ** Sequences with cluster assignment output with new names 10 | ** Tree modified to contain new names 11 | ** new names have form: Clust(C)_(SequenceName) where C = cluster number, e.g. Clust25_139320 12 | ------------------------- 13 | Output sequences = C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866_EU1866.treeforCPT_clusterPicks.fas 14 | Output tree= C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.treeforCPT_clusterPicks.nwk 15 | Output figtree= C:\Users\Manon\Documents\Project\CPT_Write-up\ClusterTutorial\EU1866.treeforCPT_clusterPicks.nwk.figTree 16 | ------------------------- 17 | There are 1866 sequences 18 | Tree has 1866 tips 19 | Found 71 clusters 20 | ClusterNumber NumberOfTips NumberOfTipsCheck TipNames Bootstrap GD 21 | 1 2 2 [B.GB.1182_48_8095_20030909.DQ879092_2003, B.GB.80597.JN101915_1998] 0.998 0.01901901901901902 22 | 2 2 2 [B.CZ.82729PL1.AY694293_2000, B.CZ.86543PL1.AY694321_2001] 1.0 0.013013013013013013 23 | 3 2 2 [B.GB.67444.JN101626_1999, B.GB.73199.JN101836_2002] 1.0 0.015015015015015015 24 | 4 2 2 [B.GB.78956.JN100840_1998, B.GB.93301.JN101878_2002] 0.926 0.03003003003003003 25 | 5 2 2 [B.GB.72086.JN100900_2001, B.GB.74246.JN100899_1997] 0.984 0.04104104104104104 26 | 6 2 2 [B.GB.77754.JN101198_1999, B.GB.79261.JN100976_2003] 1.0 0.02002002002002002 27 | 7 2 2 [B.GB.81423.JN100924_2002, B.GB.99418.JN100857_2003] 0.973 0.03403403403403404 28 | 8 2 2 [B.BE.VI2681.DQ177234_2002, B.GB.94777.JN101269_1998] 0.975 0.035035035035035036 29 | 9 3 3 [B.GB.98050.JN101673_2003, B.GB.79862.JN101284_2001, B.GB.67817.JN100938_2000] 0.917 0.043043043043043044 30 | 10 2 2 [B.BE.Q34.DQ061392_1997, B.IT.56MUS.EU496236_2001] 0.904 0.026026026026026026 31 | 11 3 3 [B.GB.90699.JN101771_2003, B.GB.77726.JN101793_2002, B.GB.81527.JN101079_2003] 1.0 0.025025025025025027 32 | 12 5 5 [B.CZ.74936PL9.AY694378_2000, B.CZ.SL10243PL10.AY694335_2000, B.CZ.87914PL1.AY694382_2000, B.CZ.83862PL1.AY694278_2000, B.CZ.85459PL1.AY694271_2000] 0.993 0.03003003003003003 33 | 13 2 2 [B.GB.86642.JN101637_2002, B.GB.92422.JN101343_2001] 0.902 0.03903903903903904 34 | 14 2 2 [B.GB.80473.JN100941_1999, B.GB.86548.JN101591_1997] 0.953 0.02902902902902903 35 | 15 2 2 [B.GB.67364.JN100826_2003, B.GB.98778.JN100725_1997] 0.997 0.015015015015015015 36 | 16 2 2 [B.GB.81432.JN101725_2000, B.GB.93296.JN101060_2001] 0.919 0.035035035035035036 37 | 17 2 2 [B.GB.75429.JN100795_2002, B.GB.96540.JN101434_2001] 0.93 0.035035035035035036 38 | 18 2 2 [B.GB.89250.JN100855_2000, B.GB.99800.JN101479_1997] 0.99 0.024024024024024024 39 | 19 3 3 [B.CZ.85600PL1.AY694273_2000, B.CZ.85522PL1.AY694281_2000, B.CZ.85534PL1.AY694272_2000] 1.0 0.002002002002002002 40 | 20 2 2 [B.GB.117850.AY362171_1999, B.GB.GB8_46R.AJ271445_1986] 0.907 0.04104104104104104 41 | 21 2 2 [B.GB.73675.JN101181_2001, B.GB.85208.JN101510_1997] 0.993 0.04104104104104104 42 | 22 2 2 [B.GB.89544.JN100806_2002, B.GB.99354.JN101168_2003] 1.0 0.006006006006006006 43 | 23 2 2 [B.GB.78634.JN101739_2002, B.GB.93560.JN101070_2003] 0.964 0.01901901901901902 44 | 24 2 2 [B.GB.84844.JN101826_2000, B.GB.99561.JN100810_2002] 1.0 0.014014014014014014 45 | 25 2 2 [B.BE.VI2626.DQ177220_2002, B.GB.78944.JN100785_2001] 0.965 0.036036036036036036 46 | 26 3 3 [B.GB.67617.JN101251_2003, B.GB.77502.JN101714_2003, B.GB.85525.JN101202_2003] 1.0 0.03203203203203203 47 | 27 2 2 [B.CZ.70948PL16.AY694250_2000, B.CZ.82516PL1.AY694288_2000] 0.938 0.044044044044044044 48 | 28 2 2 [B.GB.84710.JN100911_2000, B.GB.97425.JN100776_2003] 1.0 0.021021021021021023 49 | 29 3 3 [B.IT.58MUS.EU496238_2001, B.GB.66582.JN101213_1998, B.GB.81580.JN101293_1998] 0.994 0.035035035035035036 50 | 30 2 2 [B.GB.71430.JN101115_1997, B.GB.81920.JN101219_2002] 0.98 0.04104104104104104 51 | 31 5 5 [B.GB.77801.JN101755_2001, B.GB.91436.JN101406_1998, B.GB.92656.JN101265_1999, B.IT.1182_48_6231_20030930.DQ878798_2003, B.IT.65MUS.EU496245_2001] 0.903 0.044044044044044044 52 | 32 6 6 [B.GB.clA_s7_n_y03.EU817066_2003, B.GB.clA_s11_n_y98.EU817049_1998, B.GB.clA_s19_n_y03.EU817057_2003, B.GB.clA_s3_n_y01.EU817062_2001, B.GB.clA_s12_n_y03.EU817050_2003, B.GB.clA_s20_n_y01.EU817059_2001] 1.0 0.023023023023023025 53 | 33 2 2 [B.BE.VI2687.DQ177228_2002, B.BE.VI339.DQ177224_1989] 0.901 0.028028028028028028 54 | 34 2 2 [B.GB.78918.JN100676_1997, B.GB.88379.JN101511_2002] 1.0 0.02002002002002002 55 | 35 2 2 [B.DE.1182_48_4238_20030513.DQ878469_2003, B.DE.1182_48_4240_20030513.DQ878471_2003] 0.999 0.005005005005005005 56 | 36 2 2 [B.FR.1182_48_3262_20030729.DQ878166_2003, B.FR.1182_48_3297_20030930.DQ878203_2003] 1.0 0.022022022022022022 57 | 37 2 2 [B.GR.1182_48_5097_20030901.DQ878593_2003, B.GR.1182_48_5098_20030925.DQ878594_2003] 0.964 0.04004004004004004 58 | 38 2 2 [B.DE.1182_48_4215_20030512.DQ878448_2003, B.DE.ID1083_GT2.GU271161_2002] 0.998 0.012012012012012012 59 | 39 2 2 [B.DE.1182_48_4137_20030320.DQ878368_2003, B.DE.1182_48_4176_20030506.DQ878410_2003] 0.998 0.03403403403403404 60 | 40 6 6 [B.GB.67840.JN101388_2000, B.GB.clB_s34_n_y03.EU817080_2003, B.GB.94935.JN100995_2003, B.GB.clB_s26_n_y02.EU817072_2002, B.GB.clB_s35_n_y01.EU817081_2001, B.GB.clB_s33_n_y00.EU817079_2000] 1.0 0.015015015015015015 61 | 41 2 2 [B.CZ.83315PL1.AY694284_2000, B.CZ.80110PL7.AY694323_2001] 0.992 0.028028028028028028 62 | 42 3 3 [B.GB.68766.JN100981_2003, B.GB.89288.JN101121_2003, B.GB.97209.JN101418_2003] 0.967 0.036036036036036036 63 | 43 5 5 [B.GB.76091.JN101249_2003, B.GB.66215.JN100858_2003, B.GB.80439.JN101149_2003, B.GB.84479.JN101925_2003, B.GB.83164.JN101313_2002] 0.978 0.035035035035035036 64 | 44 3 3 [B.GB.98979.JN100701_2000, B.GB.66386.JN100703_2002, B.GB.92457.JN101143_2003] 0.962 0.03403403403403404 65 | 45 2 2 [B.CZ.87053PL1.AY694344_2000, B.GB.87781.JN101429_2001] 1.0 0.014014014014014014 66 | 46 2 2 [B.GB.79271.JN101525_2002, B.GB.79911.JN101167_1999] 0.98 0.03803803803803804 67 | 47 2 2 [B.CZ.87933PL1.AY694377_2000, B.CZ.SL15556PL1.AY694295_2000] 0.988 0.042042042042042045 68 | 48 2 2 [B.GB.71435.JN101658_2001, B.GB.95500.JN100856_2002] 1.0 0.011011011011011011 69 | 49 2 2 [B.GB.84724.JN101059_2000, B.GB.91777.JN101452_2001] 1.0 0.008008008008008008 70 | 50 3 3 [B.CZ.87009PL1.AY694339_2000, B.CZ.84453PL2.AY694265_2000, B.CZ.84878PL1.AY694276_2000] 0.985 0.023023023023023025 71 | 51 2 2 [B.BE.M24.DQ061388_1996, B.GB.96768.JN100825_1999] 0.926 0.031031031031031032 72 | 52 2 2 [B.IT.36MUS.EU496216_2001, B.IT.39MUS.EU496219_2001] 0.904 0.043043043043043044 73 | 53 2 2 [B.GB.1182_48_8009_20030506.DQ879054_2003, B.GB.71670.JN101435_2002] 0.975 0.037037037037037035 74 | 54 2 2 [B.CZ.85755PL1.AY694301_2000, B.DE.1182_48_4122_20030409.DQ878353_2003] 0.999 0.026026026026026026 75 | 55 2 2 [B.GB.100346.JN100671_2002, B.GB.70066.JN101924_2003] 0.998 0.02702702702702703 76 | 56 2 2 [B.CZ.52540PL14.AY694308_2000, B.CZ.79664PL1.AY694292_2000] 1.0 0.018018018018018018 77 | 57 2 2 [B.ES.1182_48_7098_20030714.DQ878951_2003, B.ES.2_1_99.AY188569_1999] 0.999 0.03803803803803804 78 | 58 2 2 [B.FR.1182_48_3149_20030429.DQ878060_2003, B.FR.1182_48_3258_20030812.DQ878162_2003] 1.0 0.031031031031031032 79 | 59 2 2 [B.FR.1182_48_3195_20030512.DQ878105_2003, B.FR.1182_48_3212_20030731.DQ878122_2003] 1.0 0.01001001001001001 80 | 60 2 2 [B.DE.1182_48_4002_20030311.DQ878235_2003, B.DE.1182_48_4174_20030502.DQ878408_2003] 1.0 0.012012012012012012 81 | 61 2 2 [B.DE.1182_48_4054_20030430.DQ878286_2003, B.DE.1182_48_4231_20030618.DQ878463_2003] 1.0 0.006006006006006006 82 | 62 2 2 [B.FR.1182_48_3169_20030409.DQ878078_2003, B.FR.1182_48_3303_20030911.DQ878207_2003] 1.0 0.003003003003003003 83 | 63 2 2 [B.DE.1182_48_4261_20030530.DQ878493_2003, B.DE.ID1561_GT2.GU271167_2002] 0.996 0.015015015015015015 84 | 64 3 3 [B.GB.75704.JN101005_2002, B.GB.82650.JN101373_2000, B.GB.98537.JN101671_2003] 1.0 0.009009009009009009 85 | 65 3 3 [B.DE.1182_48_4109_20030304.DQ878339_2003, B.DE.1182_48_4050_20030218.DQ878283_2003, B.DE.1182_48_4110_20030311.DQ878340_2003] 0.995 0.04004004004004004 86 | 66 2 2 [B.GB.91351.JN100798_2000, B.GB.98260.JN101870_2001] 0.92 0.03403403403403404 87 | 67 2 2 [B.GB.87761.JN101601_2003, B.GB.MM33d391_P4.HM586190_2001] 0.998 0.014014014014014014 88 | 68 3 3 [B.GB.A295.AF494112_1995, B.GB.B4-bp1.AF494110_1998, B.GB.C198.AF494111_1998] 0.943 0.03903903903903904 89 | 69 2 2 [B.GB.77183.JN101935_2003, B.GB.80117.JN101943_2003] 0.999 0.016016016016016016 90 | 70 3 3 [B.GB.76784.JN101000_2000, B.GB.87532.JN101089_2003, B.GB.90653.JN101465_2003] 0.997 0.021021021021021023 91 | 71 2 2 [B.GB.71329.JN101640_2000, B.GB.93775.JN101884_2003] 0.982 0.031031031031031032 92 | ------------------------- 93 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster12_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.CZ.74936PL9.AY694378_2000 2 | B.CZ.SL10243PL10.AY694335_2000 3 | B.CZ.87914PL1.AY694382_2000 4 | B.CZ.83862PL1.AY694278_2000 5 | B.CZ.85459PL1.AY694271_2000 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster31_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.77801.JN101755_2001 2 | B.GB.91436.JN101406_1998 3 | B.GB.92656.JN101265_1999 4 | B.IT.1182_48_6231_20030930.DQ878798_2003 5 | B.IT.65MUS.EU496245_2001 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster32_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.clA_s7_n_y03.EU817066_2003 2 | B.GB.clA_s11_n_y98.EU817049_1998 3 | B.GB.clA_s19_n_y03.EU817057_2003 4 | B.GB.clA_s3_n_y01.EU817062_2001 5 | B.GB.clA_s12_n_y03.EU817050_2003 6 | B.GB.clA_s20_n_y01.EU817059_2001 7 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster40_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.67840.JN101388_2000 2 | B.GB.clB_s34_n_y03.EU817080_2003 3 | B.GB.94935.JN100995_2003 4 | B.GB.clB_s26_n_y02.EU817072_2002 5 | B.GB.clB_s35_n_y01.EU817081_2001 6 | B.GB.clB_s33_n_y00.EU817079_2000 7 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU1866/EU1866_EU1866.treeforCPT_clusterPicks_cluster43_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.76091.JN101249_2003 2 | B.GB.66215.JN100858_2003 3 | B.GB.80439.JN101149_2003 4 | B.GB.84479.JN101925_2003 5 | B.GB.83164.JN101313_2002 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster101_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.77420.JN101554_2006 2 | B.GB.68766.JN100981_2003 3 | B.GB.97209.JN101418_2003 4 | B.GB.70144.JN101096_2006 5 | B.GB.89288.JN101121_2003 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster121_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.IT.1182_48_6231_20030930.DQ878798_2003 2 | B.IT.65MUS.EU496245_2001 3 | B.GB.77801.JN101755_2001 4 | B.GB.91436.JN101406_1998 5 | B.GB.92656.JN101265_1999 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster124_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.CY.CY267.JF683808_2009 2 | B.CY.CY216.JF683765_2007 3 | B.CY.CY246.JF683791_2009 4 | B.GB.clA_s7_n_y03.EU817066_2003 5 | B.GB.100222.JN100794_2006 6 | B.GB.clA_s19_n_y03.EU817057_2003 7 | B.GB.clA_s5_n_y05.EU817064_2005 8 | B.GB.clA_s3_n_y01.EU817062_2001 9 | B.GB.clA_s8_n_y04.EU817067_2004 10 | B.GB.clA_s4_n_y05.EU817063_2005 11 | B.GB.clA_s11_n_y98.EU817049_1998 12 | B.GB.clA_s12_n_y03.EU817050_2003 13 | B.GB.clA_s22_n_y04.EU817061_2004 14 | B.GB.clA_s10_n_y04.EU817048_2004 15 | B.GB.clA_s21_n_y05.EU817060_2005 16 | B.GB.clA_s18_n_y05.EU817056_2005 17 | B.GB.clA_s1_n_y05.EU817047_2005 18 | B.GB.clA_s13_n_y05.EU817051_2005 19 | B.GB.clA_s9_n_y05.EU817068_2005 20 | B.GB.clA_s17_n_y05.EU817055_2005 21 | B.GB.clA_s6_n_y05.EU817065_2005 22 | B.GB.clA_s14_n_y05.EU817052_2005 23 | B.GB.clA_s16_n_y04.EU817054_2004 24 | B.GB.clA_s2_n_y05.EU817058_2005 25 | B.GB.clA_s20_n_y01.EU817059_2001 26 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster138_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.67617.JN101251_2003 2 | B.GB.85525.JN101202_2003 3 | B.CY.CY188.JF683741_2007 4 | B.GB.77502.JN101714_2003 5 | B.GB.79655.JN100780_2004 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster170_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.93560.JN101070_2003 2 | B.GB.87483.JN101890_2006 3 | B.GB.66276.JN101792_2004 4 | B.GB.90983.JN101486_2007 5 | B.GB.92247.JN101686_2004 6 | B.GB.67944.JN101323_2005 7 | B.GB.78634.JN101739_2002 8 | B.GB.95495.JN101896_2006 9 | B.GB.75888.JN101084_2005 10 | B.GB.100389.JN101100_2005 11 | B.GB.77565.JN101663_2005 12 | B.GB.94134.JN101081_2006 13 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster171_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.85374.JN100797_2007 2 | B.GB.86273.JN101404_2004 3 | B.CZ.85600PL1.AY694273_2000 4 | B.CZ.85522PL1.AY694281_2000 5 | B.CZ.85534PL1.AY694272_2000 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster178_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.BE.VI2626.DQ177220_2002 2 | B.GB.78944.JN100785_2001 3 | B.GB.74215.JN101676_2005 4 | B.GB.98658.JN101551_2005 5 | B.GB.80074.JN101810_2006 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster195_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.89578.JN101677_2006 2 | B.GB.clB_s30_n_y05.EU817076_2005 3 | B.GB.67840.JN101388_2000 4 | B.GB.clB_s34_n_y03.EU817080_2003 5 | B.GB.89742.JN101197_2004 6 | B.GB.clB_s32_n_y04.EU817078_2004 7 | B.GB.67620.JN101107_2004 8 | B.GB.clB_s27_n_y05.EU817073_2005 9 | B.GB.clB_s29_n_y04.EU817075_2004 10 | B.GB.clB_s23_e_y05.EU817069_2005 11 | B.GB.92595.JN101090_2006 12 | B.GB.clB_s24_n_y05.EU817070_2005 13 | B.GB.clB_s31_n_y05.EU817077_2005 14 | B.GB.clB_s26_n_y02.EU817072_2002 15 | B.GB.94935.JN100995_2003 16 | B.GB.clB_s35_n_y01.EU817081_2001 17 | B.GB.clB_s33_n_y00.EU817079_2000 18 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster196_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.94194.JN101436_2005 2 | B.GB.90699.JN101771_2003 3 | B.GB.97927.JN101459_2006 4 | B.GB.81527.JN101079_2003 5 | B.GB.84709.JN100948_2005 6 | B.GB.90776.JN101207_2005 7 | B.GB.77726.JN101793_2002 8 | B.GB.92178.JN101881_2005 9 | B.GB.77900.JN101895_2005 10 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster202_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.75704.JN101005_2002 2 | B.GB.82699.JN100737_2006 3 | B.GB.82650.JN101373_2000 4 | B.GB.67479.JN101053_2004 5 | B.GB.98537.JN101671_2003 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster210_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.IT.CV1136_102_07.GU969514_2007 2 | B.IT.CV1170_34_08.GU969535_2008 3 | B.IT.CV1068_133_06.GU969486_2006 4 | B.IT.CV1054_124_06.GU969484_2006 5 | B.IT.CV984_73_06.GU969495_2006 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster222_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.87022.JN100991_2006 2 | B.GB.85037.JN101741_2006 3 | B.GB.95401.JN101931_2006 4 | B.GB.91315.JN101880_2006 5 | B.GB.99939.JN101230_2006 6 | B.GB.66778.JN101390_2007 7 | B.GB.74719.JN101482_2006 8 | B.GB.96102.JN101903_2006 9 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster224_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.71102.JN101174_2007 2 | B.GB.100346.JN100671_2002 3 | B.CY.CY032.FJ388898_2005 4 | B.GB.68367.JN100665_2005 5 | B.GB.70066.JN101924_2003 6 | B.GB.79058.JN101649_2004 7 | B.GB.67719.JN100903_2005 8 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster30_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.CZ.74936PL9.AY694378_2000 2 | B.CZ.SL10243PL10.AY694335_2000 3 | B.CZ.87914PL1.AY694382_2000 4 | B.CZ.83862PL1.AY694278_2000 5 | B.CZ.85459PL1.AY694271_2000 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster33_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.ES.05SP0243938.FJ481768_2005 2 | B.GB.clC_s36_n_y02.EU817085_2002 3 | B.GB.clC_s37_n_y05.EU817083_2005 4 | B.GB.clC_s38_n_y05.EU817084_2005 5 | B.GB.clC_s39_n_y05.EU817082_2005 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster52_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.ES.06SP375981.FJ481724_2004 2 | B.GB.78259.JN101664_2006 3 | B.GB.73798.JN101733_2006 4 | B.GB.66323.JN101240_2006 5 | B.GB.74805.JN100993_2006 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster59_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.78819.JN101134_2006 2 | B.GB.67806.JN101768_2006 3 | B.GB.85950.JN100949_2006 4 | B.GB.67690.JN101153_2005 5 | B.GB.80753.JN101565_2006 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster67_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.99681.JN101492_2005 2 | B.GB.73733.JN100702_2004 3 | B.GB.76784.JN101000_2000 4 | B.GB.88278.JN101928_2005 5 | B.GB.87532.JN101089_2003 6 | B.GB.90653.JN101465_2003 7 | B.GB.100215.JN101585_2006 8 | B.GB.91074.JN101860_2006 9 | B.GB.70017.JN101347_2005 10 | B.GB.75726.JN100864_2004 11 | B.GB.89166.JN100726_2005 12 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster76_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.90600.JN101941_2005 2 | B.GB.98979.JN100701_2000 3 | B.GB.71304.JN101646_2004 4 | B.GB.66386.JN100703_2002 5 | B.GB.92457.JN101143_2003 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster78_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.98843.JN101324_1998 2 | B.GB.79202.JN101094_2006 3 | B.GB.76818.JN101805_2005 4 | B.GB.84248.JN101879_2006 5 | B.GB.66208.JN101066_2006 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster86_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.71034.JN101542_2006 2 | B.GB.80026.JN100890_2006 3 | B.GB.92351.JN101666_2005 4 | B.CZ.87053PL1.AY694344_2000 5 | B.GB.87781.JN101429_2001 6 | B.GB.85080.JN101871_2006 7 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster90_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.83454.JN100715_2007 2 | B.GB.80556.JN100690_2004 3 | B.GB.81851.JN101058_2005 4 | B.GB.72891.JN101607_2005 5 | B.GB.95835.JN100677_2006 6 | B.GB.88392.JN101780_2006 7 | B.GB.96861.JN101534_2006 8 | B.GB.92932.JN101904_2005 9 | B.ES.X2510_1.GU326114_2008 10 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/HIV/CPoutput/EU3031/EU3031_EU3031.treeforCPT_clusterPicks_cluster95_sequenceList.txt: -------------------------------------------------------------------------------- 1 | B.GB.71413.JN101645_2004 2 | B.GB.80439.JN101149_2003 3 | B.GB.84479.JN101925_2003 4 | B.GB.91251.JN101907_2006 5 | B.GB.66215.JN100858_2003 6 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/MCC_to_NWK.R: -------------------------------------------------------------------------------- 1 | # function to convert a BEAST MCC tree to a newick string 2 | # with node names as posterior probabilities 3 | # S. J. Lycett 4 | # 8 Nov 2011 5 | 6 | # 20 Sept 2013 - for use with supplementary data from paper: 7 | # Automated Analysis of Phylogenetic Clusters, Ragonnet-Cronin et al (2013) BMC Bioinformatics 8 | 9 | # 25 Sept 2013 - includes option to ladderize and force to bifuraction 10 | # 25 Sept 2013 - also assigns 0 support to nodes with no label 11 | 12 | 13 | 14 | # needs package ape 15 | library(ape) 16 | 17 | # FUNCTION DEFINITION 18 | MCC_to_NWK <- function( fname, doLadderize=FALSE, tol=1e-8, root0=TRUE ) { 19 | 20 | # read the MCC tree file from TreeAnnotator 21 | lines <- readLines(fname) 22 | 23 | # get the taxa information 24 | ts <- grep("Translate", lines)[1]+1 25 | te <- grep(";", lines)[6]-1 26 | taxaLines <- lines[ts:te] 27 | taxaTbl <- unlist(apply(as.matrix(taxaLines), 1, strsplit, " ")) 28 | taxaTbl <- t(matrix(taxaTbl, 2, length(taxaTbl)/2)) 29 | taxaTbl[,1] <- gsub("\t", "", taxaTbl[,1]) 30 | taxaTbl[,2] <- gsub("'", "", taxaTbl[,2]) 31 | taxaTbl[,2] <- gsub(",", "", taxaTbl[,2]) 32 | 33 | # get strip the tree string from the relevant line 34 | trLine <- lines[te+2] 35 | trLine <- strsplit(trLine, "\\[\\&R\\]")[[1]][2] 36 | 37 | sb <- gregexpr("\\[", trLine)[[1]] 38 | eb <- gregexpr("\\]", trLine)[[1]] 39 | 40 | # replace , by | in node names 41 | for (i in 1:length(sb)) { 42 | before <- substring(trLine, 1, sb[i]) 43 | between<- substring(trLine, sb[i]+1, eb[i]-1) 44 | after <- substring(trLine, eb[i], nchar(trLine)) 45 | between<- gsub(",", "|", between) 46 | trLine <- paste(before,between,after,sep="") 47 | } 48 | 49 | tr <- read.tree(text=trLine) 50 | 51 | if (doLadderize) { 52 | tr <- multi2di(tr) 53 | tr <- ladderize(tr, right=FALSE) 54 | einds <- which(tr$edge.length < tol) 55 | if (length(einds) > 0) { 56 | tr$edge.length[einds] <- tol 57 | } 58 | } 59 | 60 | 61 | # extract proper tip names 62 | tips <- unlist(apply(as.matrix(tr$tip.label), 1, strsplit, "\\[")) 63 | tips <- t(matrix(tips, 2, length(tips)/2)) 64 | tips <- tips[,1] 65 | tinds <- match(tips, taxaTbl[,1]) 66 | tr$tip.label <- taxaTbl[tinds,2] 67 | 68 | # extract posterior support 69 | for (i in 1:length(tr$node.label)) { 70 | jj <- gregexpr("posterior=([0-9]+\\.)?[0-9Ee\\-]+", tr$node.label[i]) 71 | js <- jj[[1]] 72 | je <- js + attributes(jj[[1]])$match.length-1 73 | nn <- substring(tr$node.label[i], js, je) 74 | nn <- gsub("posterior=", "", nn) 75 | tr$node.label[i] <- nn 76 | } 77 | 78 | pp <- as.numeric(tr$node.label) 79 | inds <- which(!is.finite(pp)) 80 | if (length(inds) > 0) { 81 | pp[inds] <- 0 82 | } 83 | tr$node.label <- format(pp, digits=4) 84 | 85 | 86 | 87 | if (root0) { 88 | # set support at root to 0 for cluster picker 89 | tr$node.label[1] <- "0.000" 90 | trString <- write.tree(tr) 91 | 92 | # this string should end with support:root length 93 | trString <- gsub(";","",trString) 94 | trString <- paste(trString, ":0.0;", sep="") 95 | } else { 96 | # remove last support value - this is not usually a good idea 97 | # so not doing it now 98 | 99 | trString <- write.tree(tr) 100 | 101 | #lastEl <- strsplit(trString, "\\)")[[1]] 102 | #lastEl <- lastEl[length(lastEl)] 103 | #trString <- gsub(lastEl, ";", trString, fixed=TRUE) 104 | } 105 | 106 | outName <- paste(fname, ".posterior.nwk", sep="") 107 | write(trString, file=outName) 108 | #write.tree(tr, file=outName) 109 | 110 | print( paste("Newick tree written to",outName) ) 111 | 112 | # uncomment the line below if you actually want the tree object returned to the R-workspace 113 | # return( tr ) 114 | } 115 | 116 | ############################################################### 117 | # EXAMPLE USE OF FUNCTION 118 | ############################################################### 119 | 120 | mccName <- "h3n2_1027_beast_mcc.tre" 121 | MCC_to_NWK(mccName) 122 | 123 | 124 | 125 | 126 | 127 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/PandemicFlu/CP_results_70_70_002_10/h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_log.txt: -------------------------------------------------------------------------------- 1 | ** Cluster Picker Results ** 2 | Input sequences = C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\pandemic_flu\h1n1_pandemic_492_short.fas 3 | Input tree = C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\pandemic_flu\h1n1_pandemic_492_short_beast_mcc.tre.posterior.nwk 4 | Initial support threshold= 0.7 5 | Support threshold= 0.7 6 | Genetic distance threshold= 0.02 7 | Large cluster threshold= 10 8 | ------------------------- 9 | ** Sequences with cluster assignment output with new names 10 | ** Tree modified to contain new names 11 | ** new names have form: Clust(C)_(SequenceName) where C = cluster number, e.g. Clust25_139320 12 | ------------------------- 13 | Output sequences = C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\pandemic_flu\h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks.fas 14 | Output tree= C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\pandemic_flu\h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks.nwk 15 | Output figtree= C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\pandemic_flu\h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks.nwk.figTree 16 | ------------------------- 17 | There are 492 sequences 18 | Tree has 492 tips 19 | Found 4 clusters 20 | ClusterNumber NumberOfTips NumberOfTipsCheck TipNames Bootstrap GD 21 | 1 2 2 [132|USA_SanAntonio|2009, 136|USA_Texas|2009] 1.0 9.154994049253868E-5 22 | 2 59 59 [98|USA_Texas|2009, 182|USA_Houston|2009, 110|Canada_Canada-QC|2009, 122|Mexico|2009, 192|USA_SanDiego|2009, 113|USA_Colorado|2009, 125|USA_Nebraska|2009, 133|USA_SanDiego|2009, 112|USA_CherryPoint|2009, 168|Germany|2009, 170|Canada_Canada-AB|2009, 105|USA_California|2009, 355|UK_HPA|2009, 104|USA_Brawley|2009, 362|UK_HPA|2009, 111|Canada_Canada-SK|2009, 174|Canada_Canada-SK|2009, 115|USA_Florida|2009, 124|USA_Minnesota|2009, 117|USA_Indiana|2009, 126|Netherlands|2009, 127|USA_NewMexico|2009, 120|USA_Maryland|2009, 311|UK_HPA|2009, 329|UK_HPA|2009, 325|UK_HPA|2009, 107|Canada_Canada-NS|2009, 491|Scotland|2009, 80|China_Jiangsu|2009, 372|UK_HPA|2009, 350|UK_HPA|2009, 410|UK_HPA|2009, 358|UK_HPA|2009, 354|UK_HPA|2009, 361|UK_HPA|2009, 353|UK_HPA|2009, 368|UK_HPA|2009, 364|UK_HPA|2009, 348|UK_HPA|2009, 378|UK_HPA|2009, 346|UK_HPA|2009, 400|UK_HPA|2009, 352|UK_HPA|2009, 398|UK_HPA|2009, 367|UK_HPA|2009, 295|UK_HPA|2009, 345|UK_HPA|2009, 382|UK_HPA|2009, 357|UK_HPA|2009, 360|UK_HPA|2009, 365|UK_HPA|2009, 381|UK_HPA|2009, 180|China_Guangdong|2009, 181|China_GuangzhouSB|2009, 383|UK_HPA|2009, 119|USA_Kansas|2009, 137|Canada_Toronto|2009, 318|UK_HPA|2009, 169|USA_Brownsville|2009] 0.9763717 0.0027464982147761604 23 | 3 380 380 [183|Italy|2009, 118|USA_Iowa|2009, 78|China_Hunan|2009, 200|USA_Wisconsin|2009, 173|Canada_Canada-QC|2009, 172|Canada_Canada-PQ|2009, 138|USA_Wisconsin|2009, 81|China_Nanjing|2009, 74|USA_Brownsville|2009, 302|UK_HPA|2009, 186|Mexico|2009, 301|UK_HPA|2009, 307|UK_HPA|2009, 490|Scotland|2009, 85|Mexico|2009, 101|USA_Wisconsin|2009, 95|China_Shanghai|2009, 131|USA_RhodeIsland|2009, 375|UK_HPA|2009, 96|USA_SilverSpring|2009, 262|Canada_Ontario|2009, 60|ElSalvador|2009, 390|UK_HPA|2009, 73|USA_Boston|2009, 254|Guam|2009, 356|UK_HPA|2009, 70|Thailand|2009, 270|India|2009, 344|UK_HPA|2009, 404|UK_HPA|2009, 99|Canada_Toronto|2009, 171|Canada_Canada-MB|2009, 207|Canada_Canada-SK|2009, 194|China_Shandong|2009, 166|Thailand|2009, 191|France|2009, 82|Bolivia|2009, 328|UK_HPA|2009, 123|USA_Michigan|2009, 214|Russia_Moscow|2009, 72|Colombia|2009, 260|USA_NewYork|2009, 88|USA_NewBern|2009, 175|USA_CherryPoint|2009, 57|Haiti|2009, 222|USA_SouthCarolina|2009, 264|USA_SouthCarolina|2009, 30|Jordan|2009, 139|Jordan|2009, 38|Kyrgyzstan|2009, 241|Thailand|2010, 177|USA_Craven|2009, 93|ElSalvador|2009, 198|Taiwan|2009, 8|Serbia|2009, 36|Serbia|2009, 46|Nigeria|2009, 31|Turkey|2009, 140|Turkey|2009, 142|Turkmenistan|2009, 153|Mexico|2009, 49|Russia_Moscow|2009, 265|Taiwan|2009, 149|USA_FtCarson|2009, 233|Mexico|2010, 287|USA_NewYork|2010, 277|Canada_Ontario|2009, 145|USA_California|2009, 273|Mexico|2009, 16|Mexico|2009, 224|USA_Texas|2009, 339|UK_HPA|2009, 121|USA_Massachusetts|2009, 305|UK_HPA|2009, 77|USA_Houston|2009, 494|Scotland|2009, 507|Scotland|2009, 426|UK_HPA|2009, 439|UK_HPA|2009, 504|Scotland|2009, 516|Scotland|2009, 242|Germany|2010, 86|Russia_Moscow|2009, 425|UK_HPA|2009, 431|UK_HPA|2009, 430|UK_HPA|2009, 523|Scotland|2009, 3|Belgium|2009, 532|Scotland|2010, 423|UK_HPA|2009, 527|Scotland|2009, 538|Scotland|2009, 474|Scotland|2009, 342|UK_HPA|2009, 141|Belgium|2009, 349|UK_HPA|2009, 391|UK_HPA|2009, 402|UK_HPA|2009, 493|Scotland|2009, 10|Kyrgyzstan|2009, 155|USA_NewYork|2009, 197|Singapore|2009, 75|USA_California|2009, 202|Japan|2009, 268|Thailand|2009, 143|Thailand|2009, 34|Thailand|2009, 229|Thailand|2010, 251|Thailand|2009, 434|UK_HPA|2009, 274|Netherlands|2009, 47|Russia_Lipetsk|2009, 33|Russia_Arkhangelsk|2009, 14|Russia_IIV-Anadyr|2009, 56|Russia_Perm|2009, 52|Norway|2009, 15|Russia_Magadan|2009, 29|Denmark|2009, 25|Poland|2009, 50|Netherlands|2009, 22|Estonia|2009, 230|Germany|2010, 5|Mali|2009, 289|Russia_Orenburg|2010, 240|Greece|2010, 154|Netherlands|2009, 17|Netherlands|2009, 1|Denmark|2009, 261|Norway|2009, 54|Russia_Orenburg|2009, 27|Russia_Yaroslavl|2009, 419|UK_HPA|2009, 436|UK_HPA|2009, 542|Scotland|2009, 440|UK_HPA|2009, 63|Russia_Tver|2009, 433|UK_HPA|2009, 505|Scotland|2009, 513|Scotland|2009, 32|Belgium|2009, 21|Taiwan|2009, 437|UK_HPA|2009, 37|Germany|2009, 147|USA_DistrictofColumbia|2009, 163|USA_Wisconsin|2009, 206|USA_California|2009, 76|Chile|2009, 176|Chile|2009, 294|UK_HPA|2009, 187|USA_Michigan|2009, 406|UK_HPA|2009, 384|UK_HPA|2009, 205|USA_Boston|2009, 13|Mongolia|2009, 148|Mongolia|2009, 159|USA_SanDiego|2009, 150|Guam|2009, 249|Japan|2009, 146|Cambodia|2009, 283|USA_Wisconsin|2009, 225|Russia_Tomsk|2009, 232|Russia_Karasuk|2010, 217|Russia_Novosibirsk|2009, 188|Russia_Moscow|2009, 204|Australia|2009, 267|Australia|2009, 250|Australia|2009, 371|UK_HPA|2009, 282|USA_Texas|2009, 211|USA_Houston|2009, 67|Denmark|2009, 71|USA_Bethesda|2009, 278|Russia_Russia|2009, 248|USA_Texas|2010, 39|Russia_Blagovechensk|2009, 7|Russia_Barnaul|2009, 470|Scotland|2009, 479|Scotland|2009, 257|Malaysia|2009, 271|Guam|2009, 234|Netherlands|2010, 420|UK_HPA|2009, 252|USA_Boston|2009, 477|Scotland|2009, 487|Scotland|2009, 428|UK_HPA|2009, 158|Ecuador|2009, 524|Scotland|2009, 515|Scotland|2009, 526|Scotland|2009, 530|Scotland|2009, 536|Scotland|2009, 535|Scotland|2009, 518|Scotland|2009, 529|Scotland|2009, 26|USA_Wisconsin|2009, 509|Scotland|2009, 528|Scotland|2009, 541|Scotland|2009, 508|Scotland|2009, 531|Scotland|2009, 6|Spain|2009, 245|USA_NewYork|2010, 238|USA_Texas|2010, 40|USA_Boston|2009, 235|USA_NewYork|2010, 286|Thailand|2010, 290|Russia_Moscow|2010, 293|Russia_Vladivistok|2010, 292|Mongolia|2011, 152|Nicaragua|2009, 244|Nicaragua|2010, 61|USA_Texas|2009, 41|USA_California|2009, 162|USA_Texas|2009, 19|USA_Newark|2009, 231|USA_California|2010, 48|Mexico|2009, 243|USA_California|2010, 269|USA_California|2009, 59|USA_SanDiego|2009, 156|Norway|2009, 51|USA_NewYork|2009, 12|USA_California|2009, 20|USA_Pensacola|2009, 421|UK_HPA|2009, 417|UK_HPA|2009, 418|UK_HPA|2009, 422|UK_HPA|2009, 424|UK_HPA|2009, 43|USA_DistrictofColumbia|2009, 397|UK_HPA|2009, 389|UK_HPA|2009, 471|Scotland|2009, 492|Scotland|2009, 374|UK_HPA|2009, 218|CzechRepublic|2009, 393|UK_HPA|2009, 304|UK_HPA|2009, 380|UK_HPA|2009, 385|UK_HPA|2009, 394|UK_HPA|2009, 412|UK_HPA|2009, 413|UK_HPA|2009, 411|UK_HPA|2009, 18|USA_NewYork|2009, 288|USA_Newark|2010, 185|Malaysia|2009, 24|Austria|2009, 219|USA_SanDiego|2009, 280|USA_SouthCarolina|2009, 92|USA_SanDiego|2009, 299|UK_HPA|2009, 297|UK_HPA|2009, 298|UK_HPA|2009, 522|Scotland|2009, 537|Scotland|2009, 276|Norway|2009, 237|Estonia|2010, 53|Canada_Ontario|2009, 65|USA_Wisconsin|2009, 157|Canada_Ontario|2009, 296|UK_HPA|2009, 415|UK_HPA|2009, 435|UK_HPA|2009, 429|UK_HPA|2009, 432|UK_HPA|2009, 35|Spain|2009, 64|Austria|2009, 416|UK_HPA|2009, 438|UK_HPA|2009, 300|UK_HPA|2009, 476|Scotland|2009, 189|USA_NewYork|2009, 216|USA_NewYork|2009, 386|UK_HPA|2009, 387|UK_HPA|2009, 363|UK_HPA|2009, 303|UK_HPA|2009, 108|Canada_Canada-ON|2009, 106|Canada_Canada-AB|2009, 407|UK_HPA|2009, 401|UK_HPA|2009, 399|UK_HPA|2009, 210|Guam|2009, 83|Luxembourg|2009, 91|CzechRepublic|2009, 395|UK_HPA|2009, 396|UK_HPA|2009, 89|USA_NewYork|2009, 79|Italy|2009, 359|UK_HPA|2009, 144|USA_Boston|2009, 23|USA_Texas|2009, 343|UK_HPA|2009, 259|Netherlands|2009, 459|Scotland|2009, 481|Scotland|2009, 442|Scotland|2009, 347|UK_HPA|2009, 255|China_Guangzhou|2009, 212|Malaysia|2009, 68|Japan|2009, 266|USA_Texas|2009, 366|UK_HPA|2009, 239|Austria|2010, 9|Germany|2009, 475|Scotland|2009, 511|Scotland|2009, 308|UK_HPA|2009, 335|UK_HPA|2009, 341|UK_HPA|2009, 334|UK_HPA|2009, 338|UK_HPA|2009, 331|UK_HPA|2009, 275|USA_NewYork|2009, 427|UK_HPA|2009, 534|Scotland|2009, 510|Scotland|2009, 512|Scotland|2009, 223|Taiwan|2009, 11|USA_Boston|2009, 253|USA_California|2009, 58|Russia_Russia|2009, 100|USA_Utah|2009, 44|China_Jiangsu|2009, 45|China_Nanjing|2009, 42|Russia_Chita|2009, 62|Russia_Tomsk|2009, 279|China_Shanghai|2009, 151|China_Nanjing|2009, 66|China_Zhoushan|2009, 28|China_Zhoushan|2009, 178|China_Fujian|2009, 179|China_Fuzhou|2009, 456|Scotland|2009, 480|Scotland|2009, 484|Scotland|2009, 449|Scotland|2009, 446|Scotland|2009, 450|Scotland|2009, 454|Scotland|2009, 478|Scotland|2009, 483|Scotland|2009, 414|UK_HPA|2009, 453|Scotland|2009, 458|Scotland|2009, 495|Scotland|2009, 485|Scotland|2009, 444|Scotland|2009, 448|Scotland|2009, 284|China_Zhejiang-Yiwu|2009, 285|China_Zhejiang|2009, 165|Argentina|2009, 69|Argentina|2009, 209|Chile|2009, 203|Argentina|2009, 128|USA_NewYork|2009, 208|India|2009, 263|Singapore|2009, 256|HongKong|2009, 236|Singapore|2010, 246|Singapore|2010, 525|Scotland|2009, 291|Thailand|2010, 281|Taiwan|2009, 161|Taiwan|2009, 97|Singapore|2009, 221|Singapore|2009, 4|Greece|2009, 228|Greece|2010, 377|UK_HPA|2009, 87|Myanmar|2009, 201|China_Zhejiang|2009, 215|Myanmar|2009, 195|China_Shanghai|2009, 129|USA_Ohio|2009, 317|UK_HPA|2009, 164|Japan|2009, 184|SouthKorea|2009] 0.9438828 0.0097042936922091 24 | 4 50 50 [103|USA_Arizona|2009, 135|USA_Tennessee|2009, 102|USA_Alabama|2009, 226|Canada_Toronto|2009, 167|China_Beijing|2009, 90|Canada_Ontario|2009, 199|Canada_Toronto|2009, 116|USA_Houston|2009, 313|UK_HPA|2009, 316|UK_HPA|2009, 309|UK_HPA|2009, 315|UK_HPA|2009, 134|USA_SouthCarolina|2009, 312|UK_HPA|2009, 114|UnitedKingdom|2009, 462|Scotland|2009, 457|Scotland|2009, 130|France|2009, 109|Canada_Canada-PQ|2009, 310|UK_HPA|2009, 319|UK_HPA|2009, 333|UK_HPA|2009, 324|UK_HPA|2009, 2|Ethiopia|2009, 258|Nicaragua|2009, 326|UK_HPA|2009, 320|UK_HPA|2009, 340|UK_HPA|2009, 323|UK_HPA|2009, 330|UK_HPA|2009, 322|UK_HPA|2009, 94|DominicanRepublic|2009, 220|DominicanRepublic|2009, 540|Scotland|2009, 160|DominicanRepublic|2009, 247|Estonia|2010, 521|Scotland|2009, 514|Scotland|2009, 506|Scotland|2009, 533|Scotland|2009, 55|USA_Pensacola|2009, 193|DominicanRepublic|2009, 392|UK_HPA|2009, 190|Canada_Ontario|2009, 227|Russia_Vladivostok|2009, 196|China_Sichuan|2009, 373|UK_HPA|2009, 213|Nicaragua|2009, 84|Nicaragua|2009, 272|Nicaragua|2009] 0.9934113 0.005676096310537398 25 | ------------------------- 26 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/PandemicFlu/CP_results_70_70_002_10/h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_cluster2_sequenceList.txt: -------------------------------------------------------------------------------- 1 | 98|USA_Texas|2009 2 | 182|USA_Houston|2009 3 | 110|Canada_Canada-QC|2009 4 | 122|Mexico|2009 5 | 192|USA_SanDiego|2009 6 | 113|USA_Colorado|2009 7 | 125|USA_Nebraska|2009 8 | 133|USA_SanDiego|2009 9 | 112|USA_CherryPoint|2009 10 | 168|Germany|2009 11 | 170|Canada_Canada-AB|2009 12 | 105|USA_California|2009 13 | 355|UK_HPA|2009 14 | 104|USA_Brawley|2009 15 | 362|UK_HPA|2009 16 | 111|Canada_Canada-SK|2009 17 | 174|Canada_Canada-SK|2009 18 | 115|USA_Florida|2009 19 | 124|USA_Minnesota|2009 20 | 117|USA_Indiana|2009 21 | 126|Netherlands|2009 22 | 127|USA_NewMexico|2009 23 | 120|USA_Maryland|2009 24 | 311|UK_HPA|2009 25 | 329|UK_HPA|2009 26 | 325|UK_HPA|2009 27 | 107|Canada_Canada-NS|2009 28 | 491|Scotland|2009 29 | 80|China_Jiangsu|2009 30 | 372|UK_HPA|2009 31 | 350|UK_HPA|2009 32 | 410|UK_HPA|2009 33 | 358|UK_HPA|2009 34 | 354|UK_HPA|2009 35 | 361|UK_HPA|2009 36 | 353|UK_HPA|2009 37 | 368|UK_HPA|2009 38 | 364|UK_HPA|2009 39 | 348|UK_HPA|2009 40 | 378|UK_HPA|2009 41 | 346|UK_HPA|2009 42 | 400|UK_HPA|2009 43 | 352|UK_HPA|2009 44 | 398|UK_HPA|2009 45 | 367|UK_HPA|2009 46 | 295|UK_HPA|2009 47 | 345|UK_HPA|2009 48 | 382|UK_HPA|2009 49 | 357|UK_HPA|2009 50 | 360|UK_HPA|2009 51 | 365|UK_HPA|2009 52 | 381|UK_HPA|2009 53 | 180|China_Guangdong|2009 54 | 181|China_GuangzhouSB|2009 55 | 383|UK_HPA|2009 56 | 119|USA_Kansas|2009 57 | 137|Canada_Toronto|2009 58 | 318|UK_HPA|2009 59 | 169|USA_Brownsville|2009 60 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/PandemicFlu/CP_results_70_70_002_10/h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_cluster3_sequenceList.txt: -------------------------------------------------------------------------------- 1 | 183|Italy|2009 2 | 118|USA_Iowa|2009 3 | 78|China_Hunan|2009 4 | 200|USA_Wisconsin|2009 5 | 173|Canada_Canada-QC|2009 6 | 172|Canada_Canada-PQ|2009 7 | 138|USA_Wisconsin|2009 8 | 81|China_Nanjing|2009 9 | 74|USA_Brownsville|2009 10 | 302|UK_HPA|2009 11 | 186|Mexico|2009 12 | 301|UK_HPA|2009 13 | 307|UK_HPA|2009 14 | 490|Scotland|2009 15 | 85|Mexico|2009 16 | 101|USA_Wisconsin|2009 17 | 95|China_Shanghai|2009 18 | 131|USA_RhodeIsland|2009 19 | 375|UK_HPA|2009 20 | 96|USA_SilverSpring|2009 21 | 262|Canada_Ontario|2009 22 | 60|ElSalvador|2009 23 | 390|UK_HPA|2009 24 | 73|USA_Boston|2009 25 | 254|Guam|2009 26 | 356|UK_HPA|2009 27 | 70|Thailand|2009 28 | 270|India|2009 29 | 344|UK_HPA|2009 30 | 404|UK_HPA|2009 31 | 99|Canada_Toronto|2009 32 | 171|Canada_Canada-MB|2009 33 | 207|Canada_Canada-SK|2009 34 | 194|China_Shandong|2009 35 | 166|Thailand|2009 36 | 191|France|2009 37 | 82|Bolivia|2009 38 | 328|UK_HPA|2009 39 | 123|USA_Michigan|2009 40 | 214|Russia_Moscow|2009 41 | 72|Colombia|2009 42 | 260|USA_NewYork|2009 43 | 88|USA_NewBern|2009 44 | 175|USA_CherryPoint|2009 45 | 57|Haiti|2009 46 | 222|USA_SouthCarolina|2009 47 | 264|USA_SouthCarolina|2009 48 | 30|Jordan|2009 49 | 139|Jordan|2009 50 | 38|Kyrgyzstan|2009 51 | 241|Thailand|2010 52 | 177|USA_Craven|2009 53 | 93|ElSalvador|2009 54 | 198|Taiwan|2009 55 | 8|Serbia|2009 56 | 36|Serbia|2009 57 | 46|Nigeria|2009 58 | 31|Turkey|2009 59 | 140|Turkey|2009 60 | 142|Turkmenistan|2009 61 | 153|Mexico|2009 62 | 49|Russia_Moscow|2009 63 | 265|Taiwan|2009 64 | 149|USA_FtCarson|2009 65 | 233|Mexico|2010 66 | 287|USA_NewYork|2010 67 | 277|Canada_Ontario|2009 68 | 145|USA_California|2009 69 | 273|Mexico|2009 70 | 16|Mexico|2009 71 | 224|USA_Texas|2009 72 | 339|UK_HPA|2009 73 | 121|USA_Massachusetts|2009 74 | 305|UK_HPA|2009 75 | 77|USA_Houston|2009 76 | 494|Scotland|2009 77 | 507|Scotland|2009 78 | 426|UK_HPA|2009 79 | 439|UK_HPA|2009 80 | 504|Scotland|2009 81 | 516|Scotland|2009 82 | 242|Germany|2010 83 | 86|Russia_Moscow|2009 84 | 425|UK_HPA|2009 85 | 431|UK_HPA|2009 86 | 430|UK_HPA|2009 87 | 523|Scotland|2009 88 | 3|Belgium|2009 89 | 532|Scotland|2010 90 | 423|UK_HPA|2009 91 | 527|Scotland|2009 92 | 538|Scotland|2009 93 | 474|Scotland|2009 94 | 342|UK_HPA|2009 95 | 141|Belgium|2009 96 | 349|UK_HPA|2009 97 | 391|UK_HPA|2009 98 | 402|UK_HPA|2009 99 | 493|Scotland|2009 100 | 10|Kyrgyzstan|2009 101 | 155|USA_NewYork|2009 102 | 197|Singapore|2009 103 | 75|USA_California|2009 104 | 202|Japan|2009 105 | 268|Thailand|2009 106 | 143|Thailand|2009 107 | 34|Thailand|2009 108 | 229|Thailand|2010 109 | 251|Thailand|2009 110 | 434|UK_HPA|2009 111 | 274|Netherlands|2009 112 | 47|Russia_Lipetsk|2009 113 | 33|Russia_Arkhangelsk|2009 114 | 14|Russia_IIV-Anadyr|2009 115 | 56|Russia_Perm|2009 116 | 52|Norway|2009 117 | 15|Russia_Magadan|2009 118 | 29|Denmark|2009 119 | 25|Poland|2009 120 | 50|Netherlands|2009 121 | 22|Estonia|2009 122 | 230|Germany|2010 123 | 5|Mali|2009 124 | 289|Russia_Orenburg|2010 125 | 240|Greece|2010 126 | 154|Netherlands|2009 127 | 17|Netherlands|2009 128 | 1|Denmark|2009 129 | 261|Norway|2009 130 | 54|Russia_Orenburg|2009 131 | 27|Russia_Yaroslavl|2009 132 | 419|UK_HPA|2009 133 | 436|UK_HPA|2009 134 | 542|Scotland|2009 135 | 440|UK_HPA|2009 136 | 63|Russia_Tver|2009 137 | 433|UK_HPA|2009 138 | 505|Scotland|2009 139 | 513|Scotland|2009 140 | 32|Belgium|2009 141 | 21|Taiwan|2009 142 | 437|UK_HPA|2009 143 | 37|Germany|2009 144 | 147|USA_DistrictofColumbia|2009 145 | 163|USA_Wisconsin|2009 146 | 206|USA_California|2009 147 | 76|Chile|2009 148 | 176|Chile|2009 149 | 294|UK_HPA|2009 150 | 187|USA_Michigan|2009 151 | 406|UK_HPA|2009 152 | 384|UK_HPA|2009 153 | 205|USA_Boston|2009 154 | 13|Mongolia|2009 155 | 148|Mongolia|2009 156 | 159|USA_SanDiego|2009 157 | 150|Guam|2009 158 | 249|Japan|2009 159 | 146|Cambodia|2009 160 | 283|USA_Wisconsin|2009 161 | 225|Russia_Tomsk|2009 162 | 232|Russia_Karasuk|2010 163 | 217|Russia_Novosibirsk|2009 164 | 188|Russia_Moscow|2009 165 | 204|Australia|2009 166 | 267|Australia|2009 167 | 250|Australia|2009 168 | 371|UK_HPA|2009 169 | 282|USA_Texas|2009 170 | 211|USA_Houston|2009 171 | 67|Denmark|2009 172 | 71|USA_Bethesda|2009 173 | 278|Russia_Russia|2009 174 | 248|USA_Texas|2010 175 | 39|Russia_Blagovechensk|2009 176 | 7|Russia_Barnaul|2009 177 | 470|Scotland|2009 178 | 479|Scotland|2009 179 | 257|Malaysia|2009 180 | 271|Guam|2009 181 | 234|Netherlands|2010 182 | 420|UK_HPA|2009 183 | 252|USA_Boston|2009 184 | 477|Scotland|2009 185 | 487|Scotland|2009 186 | 428|UK_HPA|2009 187 | 158|Ecuador|2009 188 | 524|Scotland|2009 189 | 515|Scotland|2009 190 | 526|Scotland|2009 191 | 530|Scotland|2009 192 | 536|Scotland|2009 193 | 535|Scotland|2009 194 | 518|Scotland|2009 195 | 529|Scotland|2009 196 | 26|USA_Wisconsin|2009 197 | 509|Scotland|2009 198 | 528|Scotland|2009 199 | 541|Scotland|2009 200 | 508|Scotland|2009 201 | 531|Scotland|2009 202 | 6|Spain|2009 203 | 245|USA_NewYork|2010 204 | 238|USA_Texas|2010 205 | 40|USA_Boston|2009 206 | 235|USA_NewYork|2010 207 | 286|Thailand|2010 208 | 290|Russia_Moscow|2010 209 | 293|Russia_Vladivistok|2010 210 | 292|Mongolia|2011 211 | 152|Nicaragua|2009 212 | 244|Nicaragua|2010 213 | 61|USA_Texas|2009 214 | 41|USA_California|2009 215 | 162|USA_Texas|2009 216 | 19|USA_Newark|2009 217 | 231|USA_California|2010 218 | 48|Mexico|2009 219 | 243|USA_California|2010 220 | 269|USA_California|2009 221 | 59|USA_SanDiego|2009 222 | 156|Norway|2009 223 | 51|USA_NewYork|2009 224 | 12|USA_California|2009 225 | 20|USA_Pensacola|2009 226 | 421|UK_HPA|2009 227 | 417|UK_HPA|2009 228 | 418|UK_HPA|2009 229 | 422|UK_HPA|2009 230 | 424|UK_HPA|2009 231 | 43|USA_DistrictofColumbia|2009 232 | 397|UK_HPA|2009 233 | 389|UK_HPA|2009 234 | 471|Scotland|2009 235 | 492|Scotland|2009 236 | 374|UK_HPA|2009 237 | 218|CzechRepublic|2009 238 | 393|UK_HPA|2009 239 | 304|UK_HPA|2009 240 | 380|UK_HPA|2009 241 | 385|UK_HPA|2009 242 | 394|UK_HPA|2009 243 | 412|UK_HPA|2009 244 | 413|UK_HPA|2009 245 | 411|UK_HPA|2009 246 | 18|USA_NewYork|2009 247 | 288|USA_Newark|2010 248 | 185|Malaysia|2009 249 | 24|Austria|2009 250 | 219|USA_SanDiego|2009 251 | 280|USA_SouthCarolina|2009 252 | 92|USA_SanDiego|2009 253 | 299|UK_HPA|2009 254 | 297|UK_HPA|2009 255 | 298|UK_HPA|2009 256 | 522|Scotland|2009 257 | 537|Scotland|2009 258 | 276|Norway|2009 259 | 237|Estonia|2010 260 | 53|Canada_Ontario|2009 261 | 65|USA_Wisconsin|2009 262 | 157|Canada_Ontario|2009 263 | 296|UK_HPA|2009 264 | 415|UK_HPA|2009 265 | 435|UK_HPA|2009 266 | 429|UK_HPA|2009 267 | 432|UK_HPA|2009 268 | 35|Spain|2009 269 | 64|Austria|2009 270 | 416|UK_HPA|2009 271 | 438|UK_HPA|2009 272 | 300|UK_HPA|2009 273 | 476|Scotland|2009 274 | 189|USA_NewYork|2009 275 | 216|USA_NewYork|2009 276 | 386|UK_HPA|2009 277 | 387|UK_HPA|2009 278 | 363|UK_HPA|2009 279 | 303|UK_HPA|2009 280 | 108|Canada_Canada-ON|2009 281 | 106|Canada_Canada-AB|2009 282 | 407|UK_HPA|2009 283 | 401|UK_HPA|2009 284 | 399|UK_HPA|2009 285 | 210|Guam|2009 286 | 83|Luxembourg|2009 287 | 91|CzechRepublic|2009 288 | 395|UK_HPA|2009 289 | 396|UK_HPA|2009 290 | 89|USA_NewYork|2009 291 | 79|Italy|2009 292 | 359|UK_HPA|2009 293 | 144|USA_Boston|2009 294 | 23|USA_Texas|2009 295 | 343|UK_HPA|2009 296 | 259|Netherlands|2009 297 | 459|Scotland|2009 298 | 481|Scotland|2009 299 | 442|Scotland|2009 300 | 347|UK_HPA|2009 301 | 255|China_Guangzhou|2009 302 | 212|Malaysia|2009 303 | 68|Japan|2009 304 | 266|USA_Texas|2009 305 | 366|UK_HPA|2009 306 | 239|Austria|2010 307 | 9|Germany|2009 308 | 475|Scotland|2009 309 | 511|Scotland|2009 310 | 308|UK_HPA|2009 311 | 335|UK_HPA|2009 312 | 341|UK_HPA|2009 313 | 334|UK_HPA|2009 314 | 338|UK_HPA|2009 315 | 331|UK_HPA|2009 316 | 275|USA_NewYork|2009 317 | 427|UK_HPA|2009 318 | 534|Scotland|2009 319 | 510|Scotland|2009 320 | 512|Scotland|2009 321 | 223|Taiwan|2009 322 | 11|USA_Boston|2009 323 | 253|USA_California|2009 324 | 58|Russia_Russia|2009 325 | 100|USA_Utah|2009 326 | 44|China_Jiangsu|2009 327 | 45|China_Nanjing|2009 328 | 42|Russia_Chita|2009 329 | 62|Russia_Tomsk|2009 330 | 279|China_Shanghai|2009 331 | 151|China_Nanjing|2009 332 | 66|China_Zhoushan|2009 333 | 28|China_Zhoushan|2009 334 | 178|China_Fujian|2009 335 | 179|China_Fuzhou|2009 336 | 456|Scotland|2009 337 | 480|Scotland|2009 338 | 484|Scotland|2009 339 | 449|Scotland|2009 340 | 446|Scotland|2009 341 | 450|Scotland|2009 342 | 454|Scotland|2009 343 | 478|Scotland|2009 344 | 483|Scotland|2009 345 | 414|UK_HPA|2009 346 | 453|Scotland|2009 347 | 458|Scotland|2009 348 | 495|Scotland|2009 349 | 485|Scotland|2009 350 | 444|Scotland|2009 351 | 448|Scotland|2009 352 | 284|China_Zhejiang-Yiwu|2009 353 | 285|China_Zhejiang|2009 354 | 165|Argentina|2009 355 | 69|Argentina|2009 356 | 209|Chile|2009 357 | 203|Argentina|2009 358 | 128|USA_NewYork|2009 359 | 208|India|2009 360 | 263|Singapore|2009 361 | 256|HongKong|2009 362 | 236|Singapore|2010 363 | 246|Singapore|2010 364 | 525|Scotland|2009 365 | 291|Thailand|2010 366 | 281|Taiwan|2009 367 | 161|Taiwan|2009 368 | 97|Singapore|2009 369 | 221|Singapore|2009 370 | 4|Greece|2009 371 | 228|Greece|2010 372 | 377|UK_HPA|2009 373 | 87|Myanmar|2009 374 | 201|China_Zhejiang|2009 375 | 215|Myanmar|2009 376 | 195|China_Shanghai|2009 377 | 129|USA_Ohio|2009 378 | 317|UK_HPA|2009 379 | 164|Japan|2009 380 | 184|SouthKorea|2009 381 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/PandemicFlu/CP_results_70_70_002_10/h1n1_pandemic_492_short_h1n1_pandemic_492_short_beast_mcc.tre.posterior_clusterPicks_cluster4_sequenceList.txt: -------------------------------------------------------------------------------- 1 | 103|USA_Arizona|2009 2 | 135|USA_Tennessee|2009 3 | 102|USA_Alabama|2009 4 | 226|Canada_Toronto|2009 5 | 167|China_Beijing|2009 6 | 90|Canada_Ontario|2009 7 | 199|Canada_Toronto|2009 8 | 116|USA_Houston|2009 9 | 313|UK_HPA|2009 10 | 316|UK_HPA|2009 11 | 309|UK_HPA|2009 12 | 315|UK_HPA|2009 13 | 134|USA_SouthCarolina|2009 14 | 312|UK_HPA|2009 15 | 114|UnitedKingdom|2009 16 | 462|Scotland|2009 17 | 457|Scotland|2009 18 | 130|France|2009 19 | 109|Canada_Canada-PQ|2009 20 | 310|UK_HPA|2009 21 | 319|UK_HPA|2009 22 | 333|UK_HPA|2009 23 | 324|UK_HPA|2009 24 | 2|Ethiopia|2009 25 | 258|Nicaragua|2009 26 | 326|UK_HPA|2009 27 | 320|UK_HPA|2009 28 | 340|UK_HPA|2009 29 | 323|UK_HPA|2009 30 | 330|UK_HPA|2009 31 | 322|UK_HPA|2009 32 | 94|DominicanRepublic|2009 33 | 220|DominicanRepublic|2009 34 | 540|Scotland|2009 35 | 160|DominicanRepublic|2009 36 | 247|Estonia|2010 37 | 521|Scotland|2009 38 | 514|Scotland|2009 39 | 506|Scotland|2009 40 | 533|Scotland|2009 41 | 55|USA_Pensacola|2009 42 | 193|DominicanRepublic|2009 43 | 392|UK_HPA|2009 44 | 190|Canada_Ontario|2009 45 | 227|Russia_Vladivostok|2009 46 | 196|China_Sichuan|2009 47 | 373|UK_HPA|2009 48 | 213|Nicaragua|2009 49 | 84|Nicaragua|2009 50 | 272|Nicaragua|2009 51 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CM_results/Asia/clustInfo_1_10.30.csv: -------------------------------------------------------------------------------- 1 | Clust_ID,Num_Seqs,"2004","2005","2006","2007","2008","2009","2010","2011","2012","Year_NA","North","South","Tropical","Region_NA","NorthAmerica","Asia","Africa","Europe","Oceania","SouthAmerica","Continent_NA" 2 | 28,37,0,0,2,35,0,0,0,0,0,0,16,0,21,0,15,21,0,1,0,0,0 3 | 2,22,17,5,0,0,0,0,0,0,0,0,18,4,0,0,0,18,0,0,4,0,0 4 | 89,73,0,0,0,0,0,0,1,56,16,0,18,0,55,0,0,68,0,5,0,0,0 5 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CM_results/Asia/log_2013-9-26_10.30.txt: -------------------------------------------------------------------------------- 1 | **Cluster Matcher** 2 | ------------------- 3 | Created 2012 by Emma Hodcroft 4 | Leigh Brown Group, Edinburgh University 5 | ======================================= 6 | 7 | Input files used: 8 | Newick file: C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\seasonal_flu\CP_results_70_70_002_10\h3n2_1027_beast_mcc.tre.posterior_clusterPicks.nwk 9 | Annotation file: C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\seasonal_flu\h3n2_1027_traits.csv 10 | Data Set 2: 11 | Newick file: 12 | 13 | The data set has 1027 sequences and 93 clusters (containing 782 sequences (76.14%)) 14 | 15 | 16 | *Preview Analysis* (No files written): 17 | 8 clusters in data set 1 (8.6%) have more than 20 sequences. 18 | Of these, 3 clusters (3.23%) have at least 50% sequences with a Continent value of Asia 19 | (Sequences without a value for Continent were not included.) 20 | Of the 132 sequences in these clusters: 21 | - 0 (0.0%) are NorthAmerica£&Asia£&Africa£&Europe£&Oceania£&SouthAmerica 22 | - 132 (100.0%) have no Continent value 23 | 24 | *FigTree Files Written*: 25 | Output Location: C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\seasonal_flu\CM_results 26 | 8 clusters in data set 1 (8.6%) have more than 20 sequences. 27 | Of these, 3 clusters (3.23%) have at least 50% sequences with a Continent value of Asia 28 | (Sequences without a value for Continent were not included.) 29 | Of the 132 sequences in these clusters: 30 | - 0 (0.0%) are NorthAmerica£&Asia£&Africa£&Europe£&Oceania£&SouthAmerica 31 | - 132 (100.0%) have no Continent value 32 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CM_results/all_clusters_details/clustInfo_1_10.32.csv: -------------------------------------------------------------------------------- 1 | Clust_ID,Num_Seqs,"2004","2005","2006","2007","2008","2009","2010","2011","2012","Year_NA","North","South","Tropical","Region_NA","NorthAmerica","Asia","Africa","Europe","Oceania","SouthAmerica","Continent_NA" 2 | 79,2,0,0,0,0,0,2,0,0,0,0,0,2,0,0,0,0,0,0,2,0,0 3 | 78,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 4 | 77,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 5 | 35,2,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 6 | 36,2,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 7 | 33,2,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 8 | 34,2,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 9 | 39,2,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 10 | 37,7,0,0,0,6,1,0,0,0,0,0,7,0,0,0,7,0,0,0,0,0,0 11 | 38,2,0,0,0,2,0,0,0,0,0,0,1,0,1,0,1,1,0,0,0,0,0 12 | 43,4,0,0,0,2,2,0,0,0,0,0,1,0,3,0,0,4,0,0,0,0,0 13 | 42,2,0,0,0,2,0,0,0,0,0,0,1,0,1,0,1,1,0,0,0,0,0 14 | 41,17,0,0,0,7,10,0,0,0,0,0,16,0,1,0,15,2,0,0,0,0,0 15 | 40,8,0,0,0,6,2,0,0,0,0,0,0,0,8,0,0,8,0,0,0,0,0 16 | 82,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,0,2,0,0,0,0 17 | 83,3,0,0,0,0,0,3,0,0,0,0,2,1,0,0,2,0,0,0,1,0,0 18 | 80,68,0,0,0,0,0,1,29,33,5,0,41,0,27,0,29,21,0,6,0,12,0 19 | 81,4,0,0,0,0,0,1,3,0,0,0,1,0,3,0,0,0,1,0,0,3,0 20 | 86,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 21 | 87,14,0,0,0,0,0,2,9,3,0,0,4,0,10,0,1,0,2,1,0,10,0 22 | 84,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 23 | 85,2,0,0,0,0,1,1,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 24 | 67,4,0,0,0,0,2,2,0,0,0,0,4,0,0,0,0,4,0,0,0,0,0 25 | 66,5,0,0,0,0,0,5,0,0,0,0,5,0,0,0,3,0,1,1,0,0,0 26 | 69,12,0,0,0,0,0,12,0,0,0,0,12,0,0,0,12,0,0,0,0,0,0 27 | 68,6,0,0,0,0,5,1,0,0,0,0,1,0,5,0,1,5,0,0,0,0,0 28 | 22,7,0,0,6,1,0,0,0,0,0,0,7,0,0,0,7,0,0,0,0,0,0 29 | 23,2,0,0,2,0,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 30 | 24,2,0,2,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,2,0,0 31 | 25,2,0,2,0,0,0,0,0,0,0,0,0,0,2,0,0,2,0,0,0,0,0 32 | 26,2,0,0,2,0,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 33 | 27,14,0,0,3,11,0,0,0,0,0,0,11,0,3,0,6,8,0,0,0,0,0 34 | 28,37,0,0,2,35,0,0,0,0,0,0,16,0,21,0,15,21,0,1,0,0,0 35 | 29,6,0,0,5,1,0,0,0,0,0,0,1,0,5,0,1,5,0,0,0,0,0 36 | 3,6,6,0,0,0,0,0,0,0,0,0,6,0,0,0,0,6,0,0,0,0,0 37 | 2,22,17,5,0,0,0,0,0,0,0,0,18,4,0,0,0,18,0,0,4,0,0 38 | 1,13,13,0,0,0,0,0,0,0,0,0,11,0,2,0,5,8,0,0,0,0,0 39 | 7,2,2,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,2,0,0 40 | 30,45,0,0,0,8,36,1,0,0,0,0,43,0,2,0,36,8,0,1,0,0,0 41 | 6,7,7,0,0,0,0,0,0,0,0,0,0,1,6,0,0,6,0,0,1,0,0 42 | 5,3,2,1,0,0,0,0,0,0,0,0,3,0,0,0,3,0,0,0,0,0,0 43 | 32,7,0,0,0,7,0,0,0,0,0,0,5,0,2,0,3,4,0,0,0,0,0 44 | 4,11,11,0,0,0,0,0,0,0,0,0,5,2,4,0,0,9,0,0,2,0,0 45 | 31,9,0,0,0,9,0,0,0,0,0,0,3,0,6,0,2,7,0,0,0,0,0 46 | 70,11,0,0,0,0,4,6,1,0,0,0,8,0,3,0,5,4,0,0,2,0,0 47 | 71,113,0,0,0,0,0,95,12,6,0,0,83,4,26,0,49,51,4,1,4,4,0 48 | 9,5,5,0,0,0,0,0,0,0,0,0,0,3,2,0,0,2,0,0,3,0,0 49 | 72,2,0,0,0,0,1,1,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 50 | 8,3,1,2,0,0,0,0,0,0,0,0,0,2,1,0,0,1,0,0,2,0,0 51 | 73,4,0,0,0,0,3,1,0,0,0,0,3,0,1,0,2,0,1,1,0,0,0 52 | 74,3,0,0,0,0,1,2,0,0,0,0,3,0,0,0,3,0,0,0,0,0,0 53 | 75,4,0,0,0,0,2,2,0,0,0,0,4,0,0,0,4,0,0,0,0,0,0 54 | 76,6,0,0,0,0,2,4,0,0,0,0,6,0,0,0,6,0,0,0,0,0,0 55 | 59,2,0,0,0,0,2,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 56 | 58,2,0,0,0,2,0,0,0,0,0,0,0,0,2,0,0,2,0,0,0,0,0 57 | 57,2,0,0,0,0,2,0,0,0,0,0,1,0,1,0,1,1,0,0,0,0,0 58 | 56,3,0,0,0,0,3,0,0,0,0,0,3,0,0,0,3,0,0,0,0,0,0 59 | 19,2,0,2,0,0,0,0,0,0,0,0,0,0,2,0,0,2,0,0,0,0,0 60 | 55,2,0,0,0,0,1,1,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 61 | 17,3,0,3,0,0,0,0,0,0,0,0,1,1,1,0,0,2,0,0,1,0,0 62 | 18,3,0,3,0,0,0,0,0,0,0,0,2,0,1,0,0,3,0,0,0,0,0 63 | 15,2,2,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,2,0,0 64 | 16,7,0,6,1,0,0,0,0,0,0,0,2,1,4,0,0,6,0,0,1,0,0 65 | 13,14,8,6,0,0,0,0,0,0,0,0,12,2,0,0,12,0,0,0,2,0,0 66 | 14,2,1,1,0,0,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 67 | 11,5,4,1,0,0,0,0,0,0,0,0,4,1,0,0,4,0,0,0,1,0,0 68 | 12,5,3,2,0,0,0,0,0,0,0,0,4,1,0,0,4,0,0,0,1,0,0 69 | 21,3,0,2,1,0,0,0,0,0,0,0,0,0,3,0,0,3,0,0,0,0,0 70 | 20,7,3,4,0,0,0,0,0,0,0,0,2,3,2,0,2,2,0,0,3,0,0 71 | 64,2,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 72 | 65,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 73 | 62,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,2,0,0,0,0,0 74 | 63,3,0,0,0,0,1,2,0,0,0,0,3,0,0,0,1,2,0,0,0,0,0 75 | 60,4,0,0,0,0,4,0,0,0,0,0,4,0,0,0,4,0,0,0,0,0,0 76 | 61,8,0,0,0,5,3,0,0,0,0,0,8,0,0,0,8,0,0,0,0,0,0 77 | 49,2,0,0,0,2,0,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 78 | 48,4,0,0,0,4,0,0,0,0,0,0,0,0,4,0,0,0,0,0,0,4,0 79 | 45,3,0,0,0,3,0,0,0,0,0,0,3,0,0,0,3,0,0,0,0,0,0 80 | 44,7,0,0,0,5,2,0,0,0,0,0,3,0,4,0,0,7,0,0,0,0,0 81 | 93,4,0,0,0,0,0,0,2,2,0,0,1,0,3,0,1,0,0,0,0,3,0 82 | 47,2,0,0,0,2,0,0,0,0,0,0,1,1,0,0,1,0,0,0,0,1,0 83 | 92,2,0,0,0,0,0,0,2,0,0,0,0,0,2,0,0,0,2,0,0,0,0 84 | 46,2,0,0,0,1,1,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,0 85 | 91,3,0,0,0,0,0,0,0,1,2,0,2,0,1,0,1,2,0,0,0,0,0 86 | 90,22,0,0,0,0,0,3,6,13,0,0,14,1,7,0,13,7,1,0,1,0,0 87 | 10,27,1,23,1,2,0,0,0,0,0,0,6,19,2,0,4,3,0,1,19,0,0 88 | 51,2,0,0,0,0,2,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 89 | 52,2,0,0,0,2,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,2,0 90 | 53,2,0,0,0,0,2,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 91 | 54,2,0,0,0,0,2,0,0,0,0,0,2,0,0,0,2,0,0,0,0,0,0 92 | 88,5,0,0,0,0,0,0,5,0,0,0,0,0,5,0,0,5,0,0,0,0,0 93 | 50,5,0,0,0,5,0,0,0,0,0,0,5,0,0,0,5,0,0,0,0,0,0 94 | 89,73,0,0,0,0,0,0,1,56,16,0,18,0,55,0,0,68,0,5,0,0,0 95 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CM_results/all_clusters_details/log_2013-9-26_10.32.txt: -------------------------------------------------------------------------------- 1 | **Cluster Matcher** 2 | ------------------- 3 | Created 2012 by Emma Hodcroft 4 | Leigh Brown Group, Edinburgh University 5 | ======================================= 6 | 7 | Input files used: 8 | Newick file: C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\seasonal_flu\CP_results_70_70_002_10\h3n2_1027_beast_mcc.tre.posterior_clusterPicks.nwk 9 | Annotation file: C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\seasonal_flu\h3n2_1027_traits.csv 10 | Data Set 2: 11 | Newick file: 12 | 13 | The data set has 1027 sequences and 93 clusters (containing 782 sequences (76.14%)) 14 | 15 | 16 | *CSV Cluster File Written*: 17 | Output Location: C:\Users\Samantha Lycett\Documents\manuscripts\cluster_picker\referee_response\to_release\seasonal_flu\CM_results 18 | 93 clusters in data set 1 (100.0%) have more than 0 sequences. 19 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster10_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/TayNguyen/TN393/2005 2 | A/California/NHRC0002/2005 3 | A/Netherlands/42/2006 4 | A/Hong_Kong/HKU44/2005 5 | A/New_York/UR06-0515/2007 6 | A/Delaware/13/2007 7 | A/Canterbury/16/2005 8 | A/Australia/NHRC0001/2005 9 | A/New_Jersey/NHRC0001/2005 10 | A/Canterbury/256/2005 11 | A/Western_Australia/66/2005 12 | A/Western_Australia/74/2005 13 | A/Waikato/15/2005 14 | A/Canterbury/253/2005 15 | A/Otago/4/2005 16 | A/Wellington/8/2005 17 | A/Canterbury/64/2005 18 | A/Australia/NHRC0013/2005 19 | A/Australia/NHRC0012/2005 20 | A/Western_Australia/68/2005 21 | A/Wellington/5/2005 22 | A/Waikato/9/2005 23 | A/Canterbury/270/2005 24 | A/Waikato/12/2005 25 | A/Wellington/4/2005 26 | A/Auckland/617/2005 27 | A/Malaysia/29930/2004 28 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster13_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Texas/NHRC0001/2005 2 | A/New_York/376/2005 3 | A/New_York/98/2004 4 | A/New_York/362/2004 5 | A/New_York/356/2004 6 | A/New_York/237/2004 7 | A/New_York/123/2004 8 | A/New_York/361/2005 9 | A/New_York/363/2004 10 | A/Canterbury/104/2005 11 | A/Wellington/2/2005 12 | A/New_York/355/2004 13 | A/New_York/388/2005 14 | A/New_York/360/2004 15 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster1_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Hong_Kong/HKU10/2004 2 | A/Hong_Kong/HKU3/2004 3 | A/Hong_Kong/HKU8/2004 4 | A/Malaysia/29997/2004 5 | A/Hong_Kong/HKU12/2004 6 | A/Hong_Kong/CUHK6554/2004 7 | A/HaNoi/HN30110/2004 8 | A/Missouri/NHRC0002/2004 9 | A/Hong_Kong/HKU2/2004 10 | A/New_York/33/2004 11 | A/Georgia/NHRC0001/2004 12 | A/New_York/10/2004 13 | A/New_York/5/2004 14 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster27_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Morioka/18/2006 2 | A/Malaysia/34015/2006 3 | A/Florida/01/2007 4 | A/Taiwan/70113/2007 5 | A/Taiwan/1452/2007 6 | A/HaNoi/BM38/2007 7 | A/Taiwan/70002/2007 8 | A/Taiwan/70307/2007 9 | A/Vermont/01/2007 10 | A/Massachusetts/12/2007 11 | A/HaNoi/N080/2007 12 | A/Hawaii/06/2006 13 | A/California/UR06-0118/2007 14 | A/Minnesota/16/2007 15 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster28_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/HaNoi/Q011/2007 2 | A/HaNoi/TX058/2007 3 | A/BacNinh/N52/2007 4 | A/Netherlands/363/2006 5 | A/HaNoi/BT17/2007 6 | A/HaNoi/N210/2007 7 | A/HaNoi/BM061/2007 8 | A/HaNoi/N015/2007 9 | A/HaNoi/N035/2007 10 | A/HaNoi/Q094/2007 11 | A/Virginia/UR06-0605/2007 12 | A/Hawaii/12/2007 13 | A/Hawaii/13/2007 14 | A/Colorado/15/2007 15 | A/HaNoi/Q039/2007 16 | A/Illinois/UR06-0600/2007 17 | A/HaNoi/N078/2007 18 | A/HaNam/Q187/2007 19 | A/HaNoi/Q148/2007 20 | A/HaNoi/N027/2007 21 | A/HaNoi/Q031/2007 22 | A/HaNoi/TX050/2007 23 | A/HaNoi/TX022/2007 24 | A/LangSon/LS156/2007 25 | A/Wisconsin/27/2007 26 | A/New_Jersey/02/2007 27 | A/Nepal/921/2006_X_PR8_X-165 28 | A/Pennsylvania/05/2007 29 | A/HaNoi/Q220/2007 30 | A/HaNoi/Q099/2007 31 | A/Alabama/UR06-0545/2007 32 | A/Wisconsin/02/2007 33 | A/Kentucky/UR06-0370/2007 34 | A/Alaska/05/2007 35 | A/Texas/UR06-0480/2007 36 | A/New_Jersey/05/2007 37 | A/New_York/03/2007 38 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster2_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Hong_Kong/HKU28/2004 2 | A/Hong_Kong/HKU21/2004 3 | A/Hong_Kong/HKU19/2004 4 | A/Hong_Kong/HKU30/2004 5 | A/Hong_Kong/CUHK35013/2004 6 | A/Hong_Kong/CUHK33677/2004 7 | A/Hong_Kong/HKU34/2004 8 | A/Hong_Kong/CUHK6422/2005 9 | A/Hong_Kong/CUHK7546/2005 10 | A/Hong_Kong/HKU38/2004 11 | A/Hong_Kong/CUHK6898/2005 12 | A/Hong_Kong/CUHK7221/2005 13 | A/Hong_Kong/HKU40/2004 14 | A/Hong_Kong/HKU42/2005 15 | A/Hong_Kong/CUHK53726/2004 16 | A/Canterbury/200/2004 17 | A/Hong_Kong/HKU25/2004 18 | A/Hong_Kong/HKU31/2004 19 | A/Hong_Kong/CUHK33851/2004 20 | A/Western_Australia/55/2004 21 | A/Queensland/42/2004 22 | A/Western_Australia/58/2004 23 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster30_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Colorado/03/2007 2 | A/Colorado/UR06-022/2007 3 | A/Guangdong/548/2008 4 | A/Guangdong/578/2008 5 | A/Guangdong/04/2007 6 | A/New_York/06/2008 7 | A/New_York/08/2008 8 | A/Netherlands/69/2007 9 | A/TayNguyen/HCM955/2007 10 | A/HaNoi/Q502/2007 11 | A/Hawaii/18/2008 12 | A/Texas/12/2008 13 | A/Texas/91/2007 14 | A/Minnesota/02/2008 15 | A/Texas/02/2008 16 | A/Boston/46/2008 17 | A/Boston/23/2008 18 | A/Tennessee/04/2008 19 | A/Mississippi/UR07-0100/2008 20 | A/Boston/2/2008 21 | A/Ohio/UR07-0140/2008 22 | A/California/09/2008 23 | A/Oregon/01/2008 24 | A/Maryland/03/2008 25 | A/Boston/3/2008 26 | A/Kentucky/UR07-0109/2008 27 | A/California/UR07-0053/2008 28 | A/Louisiana/04/2008 29 | A/Pennsylvania/PIT39/2008 30 | A/Boston/29/2008 31 | A/Hawaii/03/2008 32 | A/Texas/04/2008 33 | A/Louisiana/05/2008 34 | A/Ohio/UR07-0073/2008 35 | A/Texas/01/2008 36 | A/Texas/AF01/2007 37 | A/Iowa/02/2008 38 | A/Texas/05/2008 39 | A/Boston/39/2008 40 | A/Texas/03/2008 41 | A/Florida/10/2008 42 | A/Ohio/UR07-0035/2008 43 | A/Korea/WRAIR1391P/2009 44 | A/Cheongju/H471/2008 45 | A/Cheongju/H380/2007 46 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster41_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Mexico/UASLP-011/2008 2 | A/Mexico/UASLP-012/2008 3 | A/Mississippi/05/2008 4 | A/Texas/71/2007 5 | A/Mississippi/01/2008 6 | A/Washington/36/2007 7 | A/Arizona/10/2007 8 | A/Washington/42/2007 9 | A/Kuwait/AF03/2008 10 | A/California/UR07-0063/2008 11 | A/Mexico/UASLP-014/2008 12 | A/Kentucky/UR07-0081/2008 13 | A/Nebraska/03/2008 14 | A/California/UR07-0017/2008 15 | A/Texas/36/2007 16 | A/Idaho/10/2007 17 | A/Malaysia/1767091/2007 18 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster4_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Thailand/Siriraj-03/2004 2 | A/NamDinh/HN30119/2004 3 | A/Hong_Kong/HKU18/2004 4 | A/Hong_Kong/CUHK35117/2004 5 | A/Hong_Kong/HKU15/2004 6 | A/Hong_Kong/CUHK33894/2004 7 | A/Wellington/6/2004 8 | A/Christchurch/15/2004 9 | A/Hong_Kong/HKU22/2004 10 | A/Malaysia/29197/2004 11 | A/HaNoi/HN30147/2004 12 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster69_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Montana/04/2009 2 | A/New_York/3146/2009 3 | A/Boston/16/2009 4 | A/California/VRDL212/2009 5 | A/California/VRDL387/2009 6 | A/Oregon/08/2009 7 | A/Colorado/WRAIR1246P/2009 8 | A/California/VRDL211/2009 9 | A/California/VRDL172/2009 10 | A/California/VRDL205/2009 11 | A/California/VRDL250/2009 12 | A/California/VRDL291/2009 13 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster70_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Texas/03/2009 2 | A/Guam/WRAIR1670P/2009 3 | A/Mexico_City/WRAIR1752T/2010 4 | A/Guam/WRAIR1557P/2009 5 | A/Moscow/416/2009 6 | A/Moscow/24/2009 7 | A/DaNang/DN453/2008 8 | A/Idaho/17/2008 9 | A/Idaho/18/2008 10 | A/South_Korea/WRAIR1171P/2009 11 | A/Hawaii/47/2008 12 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster71_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Malaysia/2205714/2009 2 | A/Egypt/N11830/2009 3 | A/Egypt/N11396/2009 4 | A/California/VRDL285/2009 5 | A/New_York/4165/2009 6 | A/Australia/18/2009 7 | A/California/VRDL243/2009 8 | A/California/VRDL204/2009 9 | A/Qingdao/2181/2009 10 | A/Qingdao/2162/2009 11 | A/Qingdao/1157/2009 12 | A/Qingdao/2199/2009 13 | A/Qingdao/2144/2009 14 | A/Singapore/GP3448/2009 15 | A/Qingdao/1346/2009 16 | A/Qingdao/1158/2009 17 | A/Qingdao/1116/2009 18 | A/Qingdao/1115/2009 19 | A/Qingdao/2157/2009 20 | A/Singapore/C2009-803bV/2009 21 | A/Qingdao/1167/2009 22 | A/Boston/DOA71/2011 23 | A/Sao_Paulo/16363/2010 24 | A/Qingdao/1341/2009 25 | A/Qingdao/2200/2009 26 | A/Qingdao/1329/2009 27 | A/Qingdao/1231/2009 28 | A/Qingdao/1118/2009 29 | A/Qingdao/1295/2009 30 | A/New_York/3738/2009 31 | A/California/VRDL257/2009 32 | A/Thailand/CU-B1697/2009 33 | A/Thailand/CU-H16/2009 34 | A/New_York/3273/2009 35 | A/Australia/2/2009 36 | A/New_York/3536/2009 37 | A/New_York/3137/2009 38 | A/New_York/3542/2009 39 | A/New_York/3417/2009 40 | A/New_York/3527/2009 41 | A/District_of_Columbia/WRAIR0301/2010 42 | A/Cambodia/NHRCC00011/2009 43 | A/New_York/3918/2009 44 | A/New_York/4255/2009 45 | A/New_York/1670/2009 46 | A/California/VRDL328/2009 47 | A/Guangdong/522/2009 48 | A/Guangdong/423/2009 49 | A/California/VRDL318/2009 50 | A/New_York/1685/2009 51 | A/Washington/WRAIR1057P/2009 52 | A/Dakar/WRAIR0011T/2009 53 | A/Dakar/WRAIR0013N/2009 54 | A/California/VRDL361/2009 55 | A/Hawaii/07/2009 56 | A/Guangdong/560/2009 57 | A/New_York/3932/2009 58 | A/Qingdao/1045/2009 59 | A/Qingdao/1046/2009 60 | A/California/VRDL336/2009 61 | A/Philippines/16/2009 62 | A/South_Carolina/14/2009 63 | A/Australia/55/2009 64 | A/Korea/WRAIR1038P/2009 65 | A/Perth/16/2009 66 | A/Florida/WRAIR1241P/2009 67 | A/Hawaii/14/2009 68 | A/Hawaii/15/2009 69 | A/California/VRDL345/2009 70 | A/California/VRDL263/2009 71 | A/California/VRDL296/2009 72 | A/California/VRDL390/2009 73 | A/California/VRDL181/2009 74 | A/California/VRDL145/2009 75 | A/California/VRDL315/2009 76 | A/California/VRDL313/2009 77 | A/California/VRDL339/2009 78 | A/California/VRDL352/2009 79 | A/Texas/40/2009 80 | A/Texas/WRAIR1239P/2009 81 | A/Singapore/C2009-458V/2009 82 | A/Singapore/GP586/2009 83 | A/Singapore/C2009-518V/2009 84 | A/Nanjing/1654/2010 85 | A/Nanjing/1655/2010 86 | A/Nanjing/1663/2010 87 | A/Niigata/1147/2010 88 | A/Novosibirsk/1927/2011 89 | A/Singapore/KK581/2011 90 | A/Shantou/546/2010 91 | A/Novosibirsk/76K/2011 92 | A/Vladivostok/10/2011 93 | A/Belgrade/WRAIR2379N/2010 94 | A/Singapore/39/2009 95 | A/Singapore/H2009-332C/2009 96 | A/California/VRDL288/2009 97 | A/Thailand/CU-B110/2009 98 | A/Thailand/CU-H1285/2010 99 | A/Thailand/CU-H1443/2010 100 | A/Thailand/CU-B1672/2009 101 | A/Singapore/H2009-334C/2009 102 | A/New_York/3135/2009 103 | A/Acre/15093/2010 104 | A/Acre/26954/2010 105 | A/Rondonia/3410/2011 106 | A/California/VRDL259/2009 107 | A/California/VRDL176/2009 108 | A/California/VRDL327/2009 109 | A/Cambodia/NHRCC00003/2009 110 | A/Cambodia/NHRCC00008/2009 111 | A/California/VRDL360/2009 112 | A/New_York/3687/2009 113 | A/California/VRDL255/2009 114 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster80_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Guangdong/441/2010 2 | A/Singapore/TT384/2010 3 | A/Guangdong/429/2010 4 | A/Singapore/H2010-559C/2010 5 | A/Singapore/H2010-564C/2010 6 | A/Netherlands/009/2010 7 | A/Singapore/GP3872/2010 8 | A/Singapore/C2010-682V/2010 9 | A/District_of_Columbia/WRAIR1753P/2010 10 | A/Guangdong/322/2010 11 | A/Guangdong/460/2010 12 | A/Boston/DOA06/2011 13 | A/Singapore/GP4397/2010 14 | A/Singapore/GP4453/2010 15 | A/Denmark/105/2010 16 | A/Guangdong/94/2011 17 | A/Singapore/GP5/2011 18 | A/Singapore/H2011-140C/2011 19 | A/Singapore/GP4555/2010 20 | A/Singapore/GP380/2011 21 | A/Boston/DOA27/2011 22 | A/Ontario/018/2011 23 | A/Boston/DOA01/2011 24 | A/Mato_Grosso/11689/2011 25 | A/Sao_Paulo/11245/2011 26 | A/Ontario/003/2010 27 | A/Boston/DOA87/2011 28 | A/Singapore/KK118/2011 29 | A/Ontario/019/2011 30 | A/Boston/DOA69/2011 31 | A/Ontario/005/2010 32 | A/Ontario/014/2011 33 | A/Ontario/020/2011 34 | A/Ontario/023/2011 35 | A/Ontario/022/2011 36 | A/Ontario/017/2011 37 | A/Alabama/AF2692/2010 38 | A/Piaui/14211/2011 39 | A/Ontario/015/2011 40 | A/Ontario/006/2010 41 | A/Tocantins/4641/2011 42 | A/Sao_Paulo/32892/2011 43 | A/Distrito_Federal/40421/2011 44 | A/Sao_Paulo/11-14557/2011 45 | A/Distrito_Federal/86727/2010 46 | A/Sao_Paulo/16761/2011 47 | A/Ontario/021/2011 48 | A/Ontario/001/2010 49 | A/Singapore/KK413/2011 50 | A/Singapore/GP4278/2010 51 | A/Managua/2492-04/2010 52 | A/Mexico_City/WRAIR4139N/2010 53 | A/Mexico_City/WRAIR3571N/2010 54 | A/California/NHRC0001/2011 55 | A/Boston/DOA77/2011 56 | A/Texas/NHRC0001/2011 57 | A/Czech_Republic/114/2012 58 | A/Czech_Republic/138/2012 59 | A/Czech_Republic/130/2012 60 | A/Saint_Petersburg/RII47/2012 61 | A/Czech_Republic/126/2012 62 | A/California/NHRC0003/2011 63 | A/Boston/DOA04/2011 64 | A/Managua/3424-01/2010 65 | A/Bogota/WRAIR3457N/2010 66 | A/Mexico_City/WRAIR3570T/2010 67 | A/Ontario/004/2010 68 | A/Singapore/N1604/2009 69 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster87_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Managua/305-10/2010 2 | A/Managua/4763-03/2010 3 | A/Managua/3704-06/2010 4 | A/Managua/1155-01/2010 5 | A/Managua/3209-01/2010 6 | A/Managua/80-1/2010 7 | A/Managua/2867-01/2010 8 | A/Managua/615-02/2010 9 | A/Sao_Paulo/11-1800/2011 10 | A/Distrito_Federal/93487/2010 11 | A/Boston/DOA16/2011 12 | A/Denmark/22/2011 13 | A/Egypt/N13658/2009 14 | A/Egypt/N13654/2009 15 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster89_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Singapore/KK7/2011 2 | A/Singapore/TT558/2011 3 | A/Singapore/GP1726/2011 4 | A/Singapore/TT481/2011 5 | A/Singapore/GP1751/2011 6 | A/Singapore/TT802/2011 7 | A/Singapore/GP1406/2011 8 | A/Singapore/GP1442/2011 9 | A/Tbilisi/GNCDC0577/2012 10 | A/Czech_Republic/119/2012 11 | A/Singapore/EN401/2011 12 | A/Singapore/GP1446/2011 13 | A/Singapore/GP1084/2011 14 | A/Singapore/KK308/2011 15 | A/Tbilisi/GNCDC0557/2012 16 | A/Singapore/KK427/2011 17 | A/Singapore/GP995/2011 18 | A/Singapore/TT556/2011 19 | A/Singapore/GP1592/2011 20 | A/Singapore/TT562/2011 21 | A/Singapore/C2011-545C/2011 22 | A/Singapore/GP1098/2011 23 | A/Singapore/C2011-584V/2011 24 | A/Singapore/SGH04/2011 25 | A/Singapore/C2011-507V/2011 26 | A/Singapore/GP1155/2011 27 | A/Singapore/TT608/2011 28 | A/Singapore/GP1030/2011 29 | A/Singapore/TT766/2011 30 | A/Singapore/TT787/2011 31 | A/Singapore/GP1797/2011 32 | A/Petrozavodsk/RII01/2012 33 | A/Singapore/EN514/2011 34 | A/Singapore/KK566/2011 35 | A/Vladivostok/59/2012 36 | A/Saint-Petersburg/RII03/2012 37 | A/Astrakhan/RII65/2011 38 | A/Saint_Petersburg/RII60/2012 39 | A/Netherlands/034/2010 40 | A/Singapore/TT416/2011 41 | A/Singapore/GP898/2011 42 | A/Singapore/KK398/2011 43 | A/Singapore/TT430/2011 44 | A/Singapore/GP1655/2011 45 | A/Singapore/KK535/2011 46 | A/Singapore/H2011-808bC/2011 47 | A/Singapore/TT815/2011 48 | A/Singapore/KK505/2011 49 | A/Singapore/TT879/2011 50 | A/Moscow/02/2012 51 | A/Ekaterinburg/RII06/2012 52 | A/Saint_Petersburg/RII16/2012 53 | A/Novosibirsk/RII09/2012 54 | A/Novosibirsk/RII25/2012 55 | A/Singapore/TT717/2011 56 | A/Czech_Republic/76/2012 57 | A/Czech_Republic/121/2012 58 | A/Singapore/TT609/2011 59 | A/Singapore/GP1684/2011 60 | A/Singapore/KK316/2011 61 | A/Singapore/TT673/2011 62 | A/Singapore/TT241/2011 63 | A/Czech_Republic/131/2012 64 | A/Singapore/GP1818/2011 65 | A/Singapore/GP1561/2011 66 | A/Singapore/TT210/2011 67 | A/Singapore/GP1382/2011 68 | A/Japan/3004/2012 69 | A/Singapore/TT869/2011 70 | A/Singapore/TT713/2011 71 | A/Singapore/TT765/2011 72 | A/Singapore/TT702/2011 73 | A/Singapore/EN122/2011 74 | -------------------------------------------------------------------------------- /docs/ClusterTutorial/SeasonalFlu/CP_results_70_70_002_10/h3n2_1027_h3n2_1027_beast_mcc.tre.posterior_clusterPicks_cluster90_sequenceList.txt: -------------------------------------------------------------------------------- 1 | A/Singapore/N1607/2009 2 | A/Singapore/C2010-304V/2010 3 | A/Egypt/N13578/2009 4 | A/Sydney/DD2-01/2010 5 | A/Singapore/GP4180/2010 6 | A/Singapore/H2010-666C/2010 7 | A/Boston/DOA24/2011 8 | A/Boston/DOA09/2011 9 | A/Boston/DOA02/2011 10 | A/Boston/DOA79/2011 11 | A/Boston/DOA51/2011 12 | A/Boston/DOA61/2011 13 | A/Boston/DOA03/2011 14 | A/Boston/DOA82/2011 15 | A/Boston/DOA64/2011 16 | A/Singapore/GP125/2011 17 | A/Boston/DOA42/2011 18 | A/Singapore/GP429/2011 19 | A/Boston/DOA20/2011 20 | A/New_York/20343/2010 21 | A/Singapore/H2010-321C/2010 22 | A/New_York/6630/2009 23 | -------------------------------------------------------------------------------- /invisBox.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/invisBox.jpg -------------------------------------------------------------------------------- /lib/about_opencsv_jar.txt: -------------------------------------------------------------------------------- 1 | About opencsv-2.3jar 2 | 3 | ---------------------------------------------------------------- 4 | 5 | This is used in the ClusterMatcher (you will need to make sure that this jar is on your build path) 6 | Here are the details: 7 | 8 | ---------------------------------------------------------------- 9 | 10 | http://sourceforge.net/projects/opencsv/ 11 | A Simple CSV Parser for Java under a commercial-friendly Apache 2.0 license 12 | 13 | ---------------------------------------------------------------- 14 | 15 | Details of Apache License for opencsv: 16 | 17 | http://www.apache.org/licenses/LICENSE-2.0.html 18 | Apache License 19 | 20 | Version 2.0, January 2004 21 | 22 | http://www.apache.org/licenses/ 23 | 24 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 25 | 26 | 1. 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While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. 70 | 71 | END OF TERMS AND CONDITIONS -------------------------------------------------------------------------------- /lib/opencsv-2.3.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/lib/opencsv-2.3.jar -------------------------------------------------------------------------------- /pressIco.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/pressIco.jpg -------------------------------------------------------------------------------- /release/ClustMatch1.2.7.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/release/ClustMatch1.2.7.jar -------------------------------------------------------------------------------- /release/ClusterPickerGUI_1.2.5.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/release/ClusterPickerGUI_1.2.5.jar -------------------------------------------------------------------------------- /release/ClusterPicker_1.2.5.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/emmahodcroft/cluster-picker-and-cluster-matcher/ba05e5294314e17a4b7fb19dbe926a6a50b8842c/release/ClusterPicker_1.2.5.jar -------------------------------------------------------------------------------- /release/about_the_jars.txt: -------------------------------------------------------------------------------- 1 | --------------------------------------------------------- 2 | About these jars 3 | Updated 7 Jun 2017 4 | --------------------------------------------------------- 5 | 6 | will run on Java 1.6 and above. If you are getting error messages, try updating your Java installation. 7 | 8 | ------------------- 9 | Cluster Picker jars 10 | ------------------- 11 | 12 | ClusterPicker_1.2.5.jar built on 07/06/2017 15:08 by Emma Hodcroft 13 | * Command line operation only: e.g. java -jar ClusterPicker_1.2.5.jar 14 | * single line operation: e.g. java -jar ClusterPicker_1.2.5.jar sequencesFileName.fas treeFileName.nwk 0.9 0.9 0.045 10 15 | 16 | + option to change the way genetic distance is calculated included: choices = gap (default), valid, abs, ambiguity 17 | + single line operation: e.g. java -jar ClusterPicker_1.2.5.jar sequencesFileName.fas treeFileName.nwk 0.9 0.9 0.045 10 gap 18 | 19 | 20 | 21 | ClusterPickerGUI_1.2.5.jar built on 07/06/2017 15:08 by Emma Hodcroft 22 | * Cluster Picker GUI application 23 | - option to change the way genetic distance is calculated is NOT included; default setting = gap (unchanged from earlier versions) 24 | 25 | 26 | ------------------- 27 | Cluster Matcher jar 28 | ------------------- 29 | 30 | ClustMatch1.2.7.jar built on 23/02/2016 16:14 by Emma Hodcroft - fixed annotation processing bug, csv output bug 31 | * Cluster Matcher GUI application 32 | 33 | --------------------------------------------------------- 34 | -------------------------------------------------------------------------------- /scripts/combine_CPCM.R: -------------------------------------------------------------------------------- 1 | ### combine CP/CM output 2 | ### M. Ragonnet 3 | ### 5th Feb 2014 4 | 5 | ## CM is cluster matcher 6 | ## CP is cluster picker 7 | ## the files output from each program should be in the same folder 8 | 9 | setwd("") 10 | path <- getwd() 11 | print(path) 12 | 13 | ## read the files 14 | #read the cm file 15 | txtFolder <- dir(path) 16 | inds <- grep("clustInfo", txtFolder) 17 | clustInfoFile <- txtFolder[inds] 18 | cm <- read.csv(clustInfoFile, header=TRUE) 19 | 20 | #read the CP log file 21 | cp_output <- readLines(list.files(pattern="*clusterPicks_log.txt")) 22 | cp_output2 <- cp_output[20:(length(cp_output)-1)] 23 | writeLines(cp_output2, "CP_output.txt") 24 | cp <- read.table("CP_output.txt", sep="\t", header=TRUE) 25 | colnames(cp)[1] <- "Clust_ID" 26 | 27 | # merge the files into one superfile and write to folder 28 | cluster_table <- merge(cp,cm,by=c("Clust_ID"), all=TRUE) 29 | 30 | 31 | for (line in 1:length(cluster_table[,1])){ 32 | if(cluster_table$NumberOfTips [line] != cluster_table$Num_Seqs[line]){ 33 | print("There was a problem combining the files!") 34 | } 35 | } 36 | 37 | write.csv (cluster_table, file ="cpcm.csv", row.names = FALSE) 38 | -------------------------------------------------------------------------------- /scripts/launchCPloop.py: -------------------------------------------------------------------------------- 1 | # This script launches CP on a series of nwk trees 2 | # Remember bootstraps are out of 100 for Raxml and out of 1 for FastTree!!! 3 | # M. Ragonnet 4 | # 21st June 2013 5 | 6 | import subprocess as sub 7 | import os 8 | 9 | # to launch on 100 simulated sequences and trees in the same folder 10 | 11 | for i in range(1,101): 12 | sub.call(["java", "-jar", "ClusterPicker_1.2.jar", 13 | "tree"+str(i)+"_simulatedSeqs.fas", "tree"+str(i)+".nwk", "90", "90","0.045","0"]) 14 | 15 | 16 | # to launch in folders and subfolders with structure bootstrap --> genetic distance 17 | 18 | bootstraps = [0.70,0.80,0.90, 0.95] 19 | genetic_distances =[0.015, 0.045] 20 | root = os.getcwd() 21 | 22 | for j in range(len(genetic_distances)): 23 | for i in range(len(bootstraps)): 24 | print(os.getcwd()) 25 | os.chdir(root+ "/"+str(bootstraps[i])+"/"+str(genetic_distances[j])) 26 | print (bootstraps[i]) 27 | sub.call(["java", "-jar", "ClusterPicker_1.2.jar", "fastaFile.fas", 28 | "tree.nwk", str(bootstraps[i]), str(bootstraps[i]),str(genetic_distances[j]),"0", "ambiguity"]) 29 | -------------------------------------------------------------------------------- /src/clusterMatcher/ClusPtr.java: -------------------------------------------------------------------------------- 1 | package clusterMatcher; 2 | 3 | /** Copyright 2011-2013 Emma Hodcroft 4 | * This file is part of ClusterMatcher. (Also may be referred to as 5 | * "ClustMatcher" or "ClustMatch".) 6 | * 7 | * ClusterMatcher is free software: you can redistribute it and/or modify 8 | * it under the terms of the GNU General Public License as published by 9 | * the Free Software Foundation, either version 3 of the License, or 10 | * any later version. 11 | * 12 | * ClusterMatcher is distributed in the hope that it will be useful, 13 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 14 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 15 | * GNU General Public License for more details. 16 | * 17 | * You should have received a copy of the GNU General Public License 18 | * along with ClusterMatcher. If not, see . 19 | */ 20 | 21 | import java.io.*; 22 | import java.util.*; 23 | import java.lang.*; 24 | import java.text.*; 25 | 26 | /** 27 | * 28 | * This is an object class that holds information about one cluster from a data set. 29 | * Each cluster is a linked-list of ClusPtr objects. The 'head' node stores information 30 | * about the cluster - the number of sequences in the cluster, the number of matches, 31 | * the cluster numbers of clusters in the other data set that match this cluster, the 32 | * newick code for the cluster, and the counts of the annotation data in the sequences in 33 | * this cluster (ex: how many females, how many homosexuals, etc) 34 | * 35 | * Each ClusPtr in the linked-list has a link to the next ClusPtr object, with the last ClusPtr object having a link to 'null' 36 | * 37 | * Each non-header node has a link to a SeqNode object that holds the info about one seq in that cluster. 38 | * 39 | * to try and represent visually: 40 | * 41 | * [cluster=66, clusterCode=((seq1:0.2,seq2..., length=2, matches=2, matchClusters=192, ...] seq -> null 42 | * next 43 | * | 44 | * v 45 | * [cluster=null, clusterCode=null, length=null, matches=null, matchClusters=null] seq -> [SeqNode 12734...] 46 | * next 47 | * | 48 | * v 49 | * [cluster=null, clusterCode=null, length=null, matches=null, matchClusters=null] seq -> [SeqNode 72361...] 50 | * next 51 | * | 52 | * v 53 | * null 54 | * 55 | * @author Emma 56 | */ 57 | public class ClusPtr { 58 | boolean verbose = false; 59 | ClusPtr next = null; //links to the next ClusPtr object in the linked-list (end points to null) 60 | String cluster = ""; //only in header - stores the number of this cluster 61 | SeqNode seq = null; // pointer to the seqNode in this cluster - only stored in each non-header node 62 | String clusterCode = ""; //only stored in header node - the tree code for this cluster 63 | int length = 0; //the number of sequences in this cluster -only stored in the 'header' node for each cluster 64 | int matches = 0; //only stored in header ndoe - number of sequences that have matches in the other dataset 65 | String matchClusters=""; //the cluster numbers of the sequences from the other dataset that match sequences in this cluster - only header 66 | String [][] annotCounts = null; //only header - stores the field variables and the the value for each sequence in the cluster 67 | 68 | public ClusPtr() 69 | { 70 | 71 | } 72 | 73 | public ClusPtr(SeqNode sn) 74 | { 75 | seq = sn; 76 | next = null; 77 | } 78 | 79 | //have we counted up the annotations present in the sequences in this cluster? 80 | public boolean hasAnnotCounts() 81 | { 82 | if(annotCounts==null) 83 | return false; 84 | return true; 85 | } 86 | 87 | //returns the cluster numbers for the clusters in the other data set that match this one 88 | public String[] getMatchClusters() 89 | { 90 | if(matchClusters.isEmpty()) 91 | return null; 92 | return matchClusters.split(","); 93 | } 94 | 95 | //updates the data on the annotations present in a cluster... 96 | //after the annotations have been added to the seqnode sn 97 | //the total anntoation counts for the cluster that 'sn' in is are updated 98 | public void updateClusterAnnots(SeqNode sn) 99 | { 100 | if(annotCounts == null) 101 | { 102 | String[] annotF = sn.getAnnotFields(); 103 | annotCounts = new String[length+1][annotF.length]; 104 | System.arraycopy(annotF, 0, annotCounts[0], 0, annotCounts[0].length); 105 | int j=0; 106 | while(jmax) 180 | max=copy[j][i]; 181 | } 182 | copy[0][i] = max; 183 | } 184 | 185 | for(int i=0; i=perc) 267 | return true; 268 | else 269 | return false; 270 | } 271 | else 272 | System.out.println("***ERROR*** A field was chosen for cluster selection that doesn't exist!"); 273 | return false; 274 | } 275 | else 276 | return false; 277 | } 278 | 279 | //I got this code online... from a forum, after searching something like 'round decimal places in java' 280 | private double roundTwoDecimals(double d) 281 | { 282 | DecimalFormat twoDForm = new DecimalFormat("#.##"); 283 | return Double.valueOf(twoDForm.format(d)); 284 | } 285 | 286 | /*debug 287 | * 288 | */ 289 | private void printMatrix(String[][] ac) 290 | { 291 | for(int i=0; i. 19 | */ 20 | 21 | import java.io.*; 22 | import java.util.*; 23 | 24 | /** 25 | * The outline for this class is based upon Samantha Lycett's class 'ReadFasFile' 26 | * @author Emma 27 | */ 28 | public class ReadNewick { 29 | 30 | private String filename; 31 | private boolean open = false; 32 | private Scanner dataFile; 33 | 34 | private String line = "x"; 35 | 36 | //////////////////////////////////////////////////////////////// 37 | // constructors 38 | 39 | public ReadNewick() { 40 | } 41 | 42 | public ReadNewick(String filename) { 43 | this.filename = filename; 44 | } 45 | 46 | /////////////////////////////////////////////////////////////// 47 | // methods 48 | 49 | public void setFilename(String filename) { 50 | this.filename = filename; 51 | } 52 | 53 | public void openFile() throws FileNotFoundException 54 | { 55 | File inputFile = new File(filename); 56 | try { 57 | // set up scanner to read one line at a time 58 | dataFile = new Scanner(inputFile).useDelimiter("\n"); 59 | open = true; 60 | } catch (FileNotFoundException e) { 61 | String error =""; 62 | if(filename==null || filename.isEmpty()) 63 | error = "No file name specified!"; 64 | else 65 | error = "Sorry file " + filename + " not found"; 66 | System.out.println(error); 67 | open = false; 68 | throw new FileNotFoundException(error); 69 | } 70 | } 71 | 72 | public void closeFile() { 73 | dataFile.close(); 74 | open = false; 75 | } 76 | 77 | public boolean hasNext() { 78 | if ( open ) { 79 | return dataFile.hasNext(); 80 | } else { 81 | return false; 82 | } 83 | } 84 | 85 | /** 86 | * next - returns the next newick tree record in the file 87 | */ 88 | public String next() { 89 | 90 | if ( open ) { 91 | 92 | if(dataFile.hasNext()) 93 | line = dataFile.next().trim(); 94 | 95 | } else { 96 | System.out.println("File "+filename+" not open"); 97 | } 98 | 99 | return line; 100 | 101 | } 102 | 103 | } 104 | -------------------------------------------------------------------------------- /src/clusterMatcher/SeqNode.java: -------------------------------------------------------------------------------- 1 | package clusterMatcher; 2 | 3 | /** Copyright 2011-2013 Emma Hodcroft 4 | * This file is part of ClusterMatcher. (Also may be referred to as 5 | * "ClustMatcher" or "ClustMatch".) 6 | * 7 | * ClusterMatcher is free software: you can redistribute it and/or modify 8 | * it under the terms of the GNU General Public License as published by 9 | * the Free Software Foundation, either version 3 of the License, or 10 | * any later version. 11 | * 12 | * ClusterMatcher is distributed in the hope that it will be useful, 13 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 14 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 15 | * GNU General Public License for more details. 16 | * 17 | * You should have received a copy of the GNU General Public License 18 | * along with ClusterMatcher. If not, see . 19 | */ 20 | 21 | /** 22 | * This is an object class that holds information about one sequence - its ID, the cluster it's in, 23 | * any matching sequences in the other data set, and it's annotation values 24 | * 25 | * @author Emma 26 | */ 27 | public class SeqNode { 28 | private String id, prefix, longID; 29 | // for a sequence 'Clust22_1443' id=1443, prefix=Clust22, longID=Clust22_1443 30 | private String cluster; //cluster = 22 (as a String!!) 31 | private String match="", fullMatch=""; //contains the match to this sequence from the other data base, and its full name 32 | private String[] annotFields; //contains the fields this seq has values for 33 | private String[] annotValues; // contains the values for the fields this seq has 34 | 35 | public SeqNode() 36 | { 37 | 38 | } 39 | 40 | public SeqNode(String i, String pref, String longI, String clus) 41 | { 42 | id = i; 43 | prefix = pref; 44 | longID = longI; 45 | cluster = clus; 46 | } 47 | 48 | public String getID() 49 | { 50 | return id; 51 | } 52 | 53 | public String getPrefix() 54 | { 55 | return prefix; 56 | } 57 | 58 | public String getLongID() 59 | { 60 | return longID; 61 | } 62 | 63 | public String getCluster() 64 | { 65 | return cluster; 66 | } 67 | 68 | public String getSeqNodeString() 69 | { 70 | return(id+" "+longID+" "+cluster); 71 | } 72 | 73 | public String getFullMatch() 74 | { 75 | return fullMatch; 76 | } 77 | 78 | public String getMatch() 79 | { 80 | return match; 81 | } 82 | 83 | public boolean hasMatch() 84 | { 85 | return !match.isEmpty(); 86 | } 87 | 88 | public void setFullMatch(String fm) 89 | { 90 | fullMatch = fm; 91 | } 92 | 93 | public void setMatch(String m) 94 | { 95 | match = m; 96 | } 97 | 98 | //adds these fields and these values to the seq node info (so can be returned as code!) 99 | public void addAnnots(String[] fields, String[] values) 100 | { 101 | annotFields = fields; 102 | for(int i=0;i. 22 | * 23 | * @author Samantha Lycett 24 | * @created 27 Sept 2013 25 | * @version 27 Sept 2013 26 | */ 27 | public class BasicSequenceTester { 28 | 29 | BasicSequence seq1; 30 | BasicSequence seq2; 31 | boolean verbose = false; 32 | 33 | 34 | public BasicSequenceTester() { 35 | 36 | } 37 | 38 | //////////////////////////////////////////////////////////////////// 39 | 40 | public void test1() { 41 | System.out.println("Test 1 : Difference between sequences with only valid characters, A, C, T, G"); 42 | seq1 = new BasicSequence("Seq1","AAAAAAAA"); 43 | seq2 = new BasicSequence("Seq2","ACTGACTG"); 44 | differenceTest(); 45 | } 46 | 47 | 48 | public void test2() { 49 | System.out.println("Test 2 : Difference between sequences with some gap characters"); 50 | seq1 = new BasicSequence("Seq1","AAAAAAAA"); 51 | seq2 = new BasicSequence("Seq2","A-~NACTG"); 52 | differenceTest(); 53 | } 54 | 55 | public void test3() { 56 | System.out.println("Test 3: Difference between sequences with some ambiguity characters"); 57 | seq1 = new BasicSequence("Seq1","AAAAAAAAAAAA"); 58 | seq2 = new BasicSequence("Seq2","AMRWSYKVHDBN"); 59 | differenceTest(); 60 | 61 | seq1 = new BasicSequence("Seq1","CCCCCCCCCCCC"); 62 | differenceTest(); 63 | 64 | seq1 = new BasicSequence("Seq1","GGGGGGGGGGGG"); 65 | differenceTest(); 66 | 67 | seq1 = new BasicSequence("Seq1","TTTTTTTTTTTT"); 68 | differenceTest(); 69 | 70 | seq1 = new BasicSequence("Seq1","MRWSYKVHDBNA"); 71 | differenceTest(); 72 | 73 | } 74 | 75 | private void differenceTest() { 76 | System.out.println("-- Difference between sequences --"); 77 | System.out.println(seq1.header()+"\t"+new String(seq1.charSeq())+"\tlength="+seq1.charSeq().length); 78 | System.out.println(seq2.header()+"\t"+new String(seq2.charSeq())+"\tlength="+seq2.charSeq().length); 79 | 80 | 81 | if (!verbose) { 82 | System.out.println("DifferenceType\tcounts\t1-2\t2-1\tfracts\t1-2\t2-1"); 83 | } 84 | 85 | 86 | String[] diffTypes = {"abs","gap","ambiguity","valid"}; 87 | 88 | for (String dt : diffTypes) { 89 | 90 | BasicSequence.setDifferenceType(dt); 91 | int diff_11 = seq1.difference(seq1); 92 | int diff_22 = seq2.difference(seq2); 93 | int diff_12 = seq1.difference(seq2); 94 | int diff_21 = seq2.difference(seq1); 95 | 96 | double fractDiff_11 = seq1.fractDifference(seq1); 97 | double fractDiff_22 = seq2.fractDifference(seq2); 98 | double fractDiff_12 = seq1.fractDifference(seq2); 99 | double fractDiff_21 = seq2.fractDifference(seq1); 100 | 101 | if (verbose) { 102 | System.out.println(""); 103 | System.out.println("-- Results for Difference Type = "+dt+" --"); 104 | System.out.println("\tCount differences:"); 105 | System.out.println("\tSeq1 vs Seq1:\t"+diff_11); 106 | System.out.println("\tSeq1 vs Seq2:\t"+diff_12); 107 | System.out.println("\tSeq2 vs Seq1:\t"+diff_21); 108 | System.out.println("\tSeq2 vs Seq2:\t"+diff_22); 109 | System.out.println(""); 110 | System.out.println("\tFraction differences:"); 111 | System.out.println("\tSeq1 vs Seq1:\t"+fractDiff_11); 112 | System.out.println("\tSeq1 vs Seq2:\t"+fractDiff_12); 113 | System.out.println("\tSeq2 vs Seq1:\t"+fractDiff_21); 114 | System.out.println("\tSeq2 vs Seq2:\t"+fractDiff_22); 115 | System.out.println(""); 116 | } else { 117 | String ddt = dt; 118 | while (ddt.length() < 10) { 119 | ddt = ddt+" "; 120 | } 121 | System.out.println(ddt+"\tcounts:\t"+diff_12+"\t"+diff_21+"\tfracts:\t"+fractDiff_12+"\t"+fractDiff_21); 122 | } 123 | } 124 | System.out.println(); 125 | } 126 | 127 | /////////////////////////////////////////////////////////////////////////////////////// 128 | 129 | public static void run(String[] args) { 130 | BasicSequenceTester tester = new BasicSequenceTester(); 131 | tester.test1(); 132 | tester.test2(); 133 | tester.test3(); 134 | } 135 | 136 | public static void main(String[] args) { 137 | run(args); 138 | } 139 | 140 | } 141 | -------------------------------------------------------------------------------- /src/clusterPicking/Node.java: -------------------------------------------------------------------------------- 1 | package clusterPicking; 2 | 3 | import java.util.*; 4 | 5 | /** 6 | * class to represent a tree node 7 | * Copyright (C) 2013 Samantha Lycett 8 | * 9 | * This file is part of ClusterPicker. 10 | * 11 | * ClusterPicker is free software: you can redistribute it and/or modify 12 | * it under the terms of the GNU General Public License as published by 13 | * the Free Software Foundation, either version 3 of the License, or 14 | * any later version. 15 | * 16 | * ClusterPicker is distributed in the hope that it will be useful, 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 19 | * GNU General Public License for more details. 20 | * 21 | * You should have received a copy of the GNU General Public License 22 | * along with ClusterPicker. If not, see . 23 | * 24 | * 25 | * @author Samantha Lycett 26 | * @created 21 Sept 2011 27 | * @version 21 Sept 2011 28 | * @version 22 Sept 2011 29 | * @version 12 Dec 2011 30 | * @version 15 Sept 2015 31 | * @version 22 Jan 2016 - EBH - changed setSupportBranchLength so that it always sets both BL and BS even if one is missing..! (fixes bug) 32 | */ 33 | public class Node implements Comparable { 34 | 35 | ///////////////////////////////////////////////////////////////////////////////////////////// 36 | // class variables and methods 37 | 38 | // node counter for labelling internal nodes 39 | private static int ncount = 1; 40 | 41 | // global tree string format setter, for use with toString() on each node 42 | private static boolean figTreeFormat = false; 43 | 44 | public static void initialiseNodeCount() { 45 | ncount = 1; 46 | } 47 | 48 | public static void setFigTreeFormat(boolean ff) { 49 | figTreeFormat = ff; 50 | } 51 | 52 | ///////////////////////////////////////////////////////////////////////////////////////////// 53 | // instance variable and methods 54 | 55 | String delim = ":"; 56 | 57 | private String name = ""; 58 | private double branchLength = 0; 59 | private double support = 0; 60 | private int totalDescends= 0; 61 | private Object trait; 62 | 63 | private Node parent; 64 | private List children; 65 | 66 | public Node() { 67 | 68 | } 69 | 70 | //////////////////////////////////////////////////////////////////////////// 71 | // getters and setters 72 | 73 | public String getName() { 74 | return name; 75 | } 76 | 77 | public void setName(String name) { 78 | this.name = name; 79 | } 80 | 81 | public double getBranchLength() { 82 | return branchLength; 83 | } 84 | 85 | public void setBranchLength(double branchLength) { 86 | this.branchLength = branchLength; 87 | } 88 | 89 | public double getSupport() { 90 | return support; 91 | } 92 | 93 | public void setSupport(double support) { 94 | this.support = support; 95 | } 96 | 97 | public Node getParent() { 98 | return parent; 99 | } 100 | 101 | public void setParent(Node parent) { 102 | this.parent = parent; 103 | } 104 | 105 | public List getChildren() { 106 | return children; 107 | } 108 | 109 | public void setChildren(List children) { 110 | this.children = children; 111 | } 112 | 113 | public void addChild(Node child) { 114 | if (children == null) { 115 | children = new ArrayList(); 116 | } 117 | this.children.add(child); 118 | } 119 | 120 | public void setTrait(Object trait) { 121 | this.trait = trait; 122 | } 123 | 124 | public Object getTrait() { 125 | return (this.trait); 126 | } 127 | 128 | ////////////////////////////////////////////////////////////////////////////////////////////// 129 | // special setters and getters 130 | 131 | public void setNameBranchLength(String txt) { 132 | String[] els = txt.split(delim); 133 | this.name = els[0]; 134 | 135 | try { 136 | this.branchLength = Double.parseDouble(els[1]); 137 | //this.support = 0; 138 | } catch (NumberFormatException e) { 139 | System.out.println("Node:setNameBranchLength - Sorry cant set "+txt); 140 | System.out.println(e.toString()); 141 | } 142 | } 143 | 144 | public void setSupportBranchLength(String txt) { 145 | String[] els = txt.split(delim); 146 | 147 | try { 148 | 149 | if (this.name.equals("")) { 150 | this.name = "Node"+ncount; 151 | ncount++; 152 | } 153 | 154 | if(els[0].length() == 0){ //if no BS, set bootstrap to 0 155 | this.support = 0.0; 156 | System.out.println("Warning: No support value, setting to 0.0"); 157 | } else { 158 | this.support = Double.parseDouble( els[0] ); 159 | } 160 | 161 | if (els[1].length() == 0){ //if no branch length, set BL to 0 162 | this.branchLength = 0.0; 163 | System.out.println("Warning: No branch length value, setting to 0.0"); 164 | } else { 165 | this.branchLength = Double.parseDouble( els[1] ); 166 | } 167 | 168 | } catch (NumberFormatException e) { 169 | System.out.println("Node:setSupportBranchLength - Sorry cant set "+txt); 170 | System.out.println(e.toString()); 171 | } 172 | } 173 | 174 | public List getAllMyChildren() { 175 | 176 | List descends = new ArrayList(); 177 | descends.add(this); 178 | 179 | if ( !isTip() ) { 180 | for (Node c : children) { 181 | descends.addAll(c.getAllMyChildren()); 182 | } 183 | } 184 | 185 | /* 186 | List toProcess= new ArrayList(); 187 | toProcess.add(this); 188 | 189 | while (toProcess.size() > 0) { 190 | Node child = toProcess.remove(0); 191 | descends.add(child); 192 | if ( !child.isTip() ) { 193 | toProcess.addAll(child.getChildren()); 194 | } 195 | } 196 | */ 197 | 198 | return descends; 199 | } 200 | 201 | 202 | //////////////////////////////////////////////////////////////////////////////////////////// 203 | // parent / child info 204 | 205 | /** 206 | * returns true if input Node n is in this children list 207 | */ 208 | public boolean hasChild(Node n) { 209 | if ( children != null) { 210 | return ( children.contains(n) ); 211 | } else { 212 | return false; 213 | } 214 | } 215 | 216 | /** 217 | * returns true if the input Node n has this as its child 218 | * should be the same as hasParent (but is not forced to be in this class) 219 | * @param n 220 | * @return 221 | */ 222 | public boolean isChildOf(Node n) { 223 | return ( hasChild(this) ); 224 | } 225 | 226 | /** 227 | * returns true if this parent is equal to input Node n 228 | * should be the same as isChildOf (but is not forced to be in this class) 229 | * @param n 230 | * @return 231 | */ 232 | public boolean hasParent(Node n) { 233 | if ( parent != null ) { 234 | return ( parent.equals(n) ); 235 | } else { 236 | return false; 237 | } 238 | } 239 | 240 | /** 241 | * returns true if no children 242 | * @return 243 | */ 244 | public boolean isTip() { 245 | if (children == null) { 246 | return true; 247 | } else if ( children.size() == 0 ) { 248 | return true; 249 | } else { 250 | return false; 251 | } 252 | } 253 | 254 | /** 255 | * returns true if no parent 256 | * @return 257 | */ 258 | public boolean isRoot() { 259 | return ( parent == null ); 260 | } 261 | 262 | /** 263 | * calculates the number of progeny recursively, stores the result in totalDescends and returns 264 | * @return 265 | */ 266 | public int calcNumProgeny() { 267 | if (isTip()) { 268 | totalDescends = 1; //0; 269 | } else { 270 | totalDescends = 0; 271 | for (Node c : children) { 272 | //totalDescends = totalDescends + 1 + c.calcNumProgeny(); 273 | totalDescends = totalDescends + c.calcNumProgeny(); 274 | } 275 | } 276 | return totalDescends; 277 | } 278 | 279 | /** 280 | * returns already calculated totalDescends 281 | * @return 282 | */ 283 | public int getNumberProgeny() { 284 | return totalDescends; 285 | } 286 | 287 | //////////////////////////////////////////////////////////////////////////////////// 288 | // Comparison methods 289 | 290 | 291 | @Override 292 | public int hashCode() { 293 | final int prime = 31; 294 | int result = 1; 295 | result = prime * result + ((name == null) ? 0 : name.hashCode()); 296 | return result; 297 | } 298 | 299 | @Override 300 | public boolean equals(Object obj) { 301 | if (this == obj) { 302 | return true; 303 | } 304 | if (obj == null) { 305 | return false; 306 | } 307 | if (!(obj instanceof Node)) { 308 | return false; 309 | } 310 | Node other = (Node) obj; 311 | if (name == null) { 312 | if (other.name != null) { 313 | return false; 314 | } 315 | } else if (!name.equals(other.name)) { 316 | return false; 317 | } 318 | return true; 319 | } 320 | 321 | @Override 322 | public int compareTo(Node b) { 323 | 324 | if ( hasChild(b) ) { 325 | return 1; 326 | } else if ( hasParent(b) ) { 327 | return -1; 328 | } else { 329 | return 0; 330 | } 331 | 332 | } 333 | 334 | /////////////////////////////////////////////////////////////////////////////////////////////////////// 335 | // display methods 336 | 337 | private String supportTxt() { 338 | if (figTreeFormat) { 339 | return ( "[&support="+this.support+"]" ); 340 | } else { 341 | return ( ""+this.support ); 342 | } 343 | } 344 | 345 | 346 | public String toString() { 347 | String txt = ""; 348 | if (isTip()) { 349 | txt = this.name + delim + this.branchLength; 350 | } else { 351 | 352 | txt = "("; 353 | for (Node c : children) { 354 | txt = txt + c.toString() + ","; 355 | } 356 | txt = txt.substring(0, txt.length()-1); 357 | txt = txt + ")"; 358 | 359 | // //txt = txt + this.support + delim + this.branchLength; 360 | txt = txt + supportTxt() + delim + this.branchLength; 361 | 362 | // experimental - not necessary 363 | //txt = txt + supportTxt() + delim + this.branchLength + "\n"; 364 | } 365 | 366 | return txt; 367 | } 368 | 369 | public String info() { 370 | StringBuffer txt = new StringBuffer(); 371 | txt.append("Name\t\t="+this.name); 372 | txt.append("\nBranchLength\t="+this.branchLength); 373 | txt.append("\nSuppport\t="+this.support); 374 | 375 | if (parent != null) { 376 | txt.append("\nParent\t\t="+this.parent.getName()); 377 | } else { 378 | txt.append("\nParent\t\t=(none) this is the root"); 379 | } 380 | 381 | if ( (children != null) && (children.size() > 0) ) { 382 | for (Node n : children) { 383 | txt.append("\nChild\t\t="+n.getName()); 384 | } 385 | } else { 386 | txt.append("\nChild\t\t=(none) this is a tip"); 387 | } 388 | txt.append("\n"); 389 | 390 | return txt.toString(); 391 | } 392 | 393 | } 394 | -------------------------------------------------------------------------------- /src/clusterPicking/ReadFasta.java: -------------------------------------------------------------------------------- 1 | package clusterPicking; 2 | 3 | import java.io.*; 4 | import java.util.*; 5 | /** 6 | * ReadFasta - class to read fasta format records from a file 7 | * Copyright (C) 2013 Samantha Lycett 8 | * 9 | * This file is part of ClusterPicker. 10 | * 11 | * ClusterPicker is free software: you can redistribute it and/or modify 12 | * it under the terms of the GNU General Public License as published by 13 | * the Free Software Foundation, either version 3 of the License, or 14 | * any later version. 15 | * 16 | * ClusterPicker is distributed in the hope that it will be useful, 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 19 | * GNU General Public License for more details. 20 | * 21 | * You should have received a copy of the GNU General Public License 22 | * along with ClusterPicker. If not, see . 23 | * 24 | * 25 | * @author Sam Lycett 26 | * @created 19 Sept 07 27 | * @version 19 Sept 07 28 | * @version 26 Sept 07 29 | * @version 4 Sept 2013 - using nextLine rather than specifying delimiter on Scanner 30 | * @version 15 Apr 2016 - using StringBuffer 31 | * 32 | */ 33 | public class ReadFasta { 34 | 35 | private String filename; 36 | private boolean open = false; 37 | private Scanner dataFile; 38 | 39 | private String recordStart = ">"; 40 | private String line = "x"; 41 | 42 | //////////////////////////////////////////////////////////////// 43 | // constructors 44 | 45 | public ReadFasta() { 46 | } 47 | 48 | public ReadFasta(String filename) { 49 | this.filename = filename; 50 | } 51 | 52 | /////////////////////////////////////////////////////////////// 53 | // methods 54 | 55 | public String recordStart() { 56 | return recordStart; 57 | } 58 | 59 | public void setFilename(String filename) { 60 | this.filename = filename; 61 | } 62 | 63 | public void openFile() { 64 | File inputFile = new File(filename); 65 | try { 66 | // set up scanner to read one line at a time 67 | //dataFile = new Scanner(inputFile).useDelimiter("\n"); 68 | dataFile = new Scanner(inputFile); // 4 Sept 2013 69 | open = true; 70 | } catch (FileNotFoundException e) { 71 | System.out.println("Sorry file "+filename+" not found"); 72 | open = false; 73 | } 74 | } 75 | 76 | public void closeFile() { 77 | dataFile.close(); 78 | open = false; 79 | } 80 | 81 | public boolean hasNext() { 82 | if ( open ) { 83 | return dataFile.hasNext(); 84 | } else { 85 | return false; 86 | } 87 | } 88 | 89 | /** 90 | * next - returns the next fasta record in the file 91 | */ 92 | public String[] next() { 93 | 94 | String[] lines = new String[2]; 95 | 96 | if ( open ) { 97 | 98 | // while not at start line 99 | while ( ( !line.startsWith(recordStart) ) && (dataFile.hasNext()) ) { 100 | //line = dataFile.next().trim(); 101 | line = dataFile.nextLine().trim(); // 4 Sept 2013 102 | } 103 | 104 | // add the header line 105 | lines[0] = line; 106 | 107 | line = "x"; 108 | String sequence = ""; 109 | 110 | // 15 apr 2016 111 | StringBuffer temp = new StringBuffer(); 112 | 113 | // while not at a start line 114 | while ( ( !line.startsWith(recordStart) ) && (dataFile.hasNext()) ) { 115 | //line = dataFile.next().trim(); 116 | line = dataFile.nextLine().trim(); // 4 Sept 2013 117 | 118 | if ( !line.startsWith(recordStart) ) { 119 | // 15 apr 2015 120 | // sequence = sequence + line; // this is very slow on long sequences 121 | 122 | // 15 apr 2016 - try like this instead 123 | temp.append(line); 124 | } 125 | } 126 | 127 | // 15 apr 2016 128 | sequence = temp.toString(); 129 | 130 | // add the sequence data 131 | lines[1] = sequence; 132 | 133 | } else { 134 | System.out.println("File "+filename+" not open"); 135 | } 136 | 137 | return lines; 138 | 139 | } 140 | 141 | } 142 | -------------------------------------------------------------------------------- /src/clusterPicking/TreeReader.java: -------------------------------------------------------------------------------- 1 | package clusterPicking; 2 | 3 | import java.io.*; 4 | import java.util.*; 5 | 6 | /** 7 | * class to read a newick tree from a file and return a tree object 8 | * Copyright (C) 2013 Samantha Lycett 9 | * 10 | * This file is part of ClusterPicker. 11 | * 12 | * ClusterPicker is free software: you can redistribute it and/or modify 13 | * it under the terms of the GNU General Public License as published by 14 | * the Free Software Foundation, either version 3 of the License, or 15 | * any later version. 16 | * 17 | * ClusterPicker is distributed in the hope that it will be useful, 18 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 19 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 20 | * GNU General Public License for more details. 21 | * 22 | * You should have received a copy of the GNU General Public License 23 | * along with ClusterPicker. If not, see . 24 | * 25 | * 26 | * @author Samantha Lycett 27 | * @created 21 Sept 2011 28 | * @version 21 Sept 2011 29 | * @version 3 Oct 2011 - modified readNextTree and readTree to keep reading in lines from file until ; 30 | * @version 15 Sept 2015 - ebh 31 | */ 32 | public class TreeReader { 33 | 34 | String fileName; 35 | Scanner inFile; 36 | boolean open = false; 37 | 38 | public TreeReader() { 39 | 40 | } 41 | 42 | public TreeReader(String f) { 43 | this.fileName = f; 44 | } 45 | 46 | ///////////////////////////////////////////////////////////////////////////////////////// 47 | 48 | public void setFileName(String f) { 49 | this.fileName = f; 50 | } 51 | 52 | public void openFile() { 53 | try { 54 | inFile = new Scanner( new File(fileName) ); 55 | open = true; 56 | } catch (IOException e) { 57 | System.out.println(e.toString()); 58 | } 59 | } 60 | 61 | public void closeFile() { 62 | inFile.close(); 63 | open = false; 64 | } 65 | 66 | public boolean hasNext() { 67 | return inFile.hasNext(); 68 | } 69 | 70 | /** 71 | * reads a newick tree line from the file, does not assume that the tree is on one line 72 | * @return 73 | */ 74 | public Tree readNextTree() { 75 | 76 | if ( (open) && (inFile.hasNext()) ) { 77 | String trLine = inFile.nextLine(); 78 | 79 | while (inFile.hasNext() && !trLine.endsWith(";")) { 80 | trLine = trLine + inFile.nextLine(); 81 | } 82 | 83 | // remove final ; 84 | trLine = trLine.replace(";", ""); 85 | 86 | Tree tr = new Tree(); 87 | tr.readTree(trLine); 88 | return tr; 89 | 90 | } else { 91 | 92 | return null; 93 | } 94 | 95 | } 96 | 97 | /** 98 | * reads a single newick tree line from a file, and closes the file. 99 | * @param s 100 | * @return 101 | */ 102 | public Tree readTree(String s) { 103 | this.fileName = s; 104 | 105 | Tree tr = null; 106 | 107 | try { 108 | inFile = new Scanner( new File(fileName) ); 109 | String trLine = inFile.nextLine(); 110 | 111 | while (inFile.hasNext() && !trLine.endsWith(";")) { 112 | trLine = trLine + inFile.nextLine(); 113 | } 114 | 115 | // remove final ; 116 | trLine = trLine.replace(";", ""); 117 | 118 | //System.out.println(trLine); 119 | 120 | tr = new Tree(); 121 | try { 122 | tr.readTree(trLine); 123 | } catch (UnsupportedOperationException e){ 124 | throw e; 125 | } 126 | 127 | inFile.close(); 128 | 129 | return tr; 130 | 131 | } catch (IOException e) { 132 | System.out.println(e.toString()); 133 | } 134 | 135 | return ( tr ); 136 | 137 | } 138 | 139 | } 140 | -------------------------------------------------------------------------------- /src/clusterPicking/TreeTester.java: -------------------------------------------------------------------------------- 1 | package clusterPicking; 2 | 3 | import java.io.*; 4 | import java.util.*; 5 | 6 | /** 7 | * class to test the Tree class 8 | * note this is only for SJL testing and the file names are hardcoded 9 | * should eventually be replaced by a JUnit test 10 | * 11 | * Copyright (C) 2013 Samantha Lycett 12 | * 13 | * This file is part of ClusterPicker. 14 | * 15 | * ClusterPicker is free software: you can redistribute it and/or modify 16 | * it under the terms of the GNU General Public License as published by 17 | * the Free Software Foundation, either version 3 of the License, or 18 | * any later version. 19 | * 20 | * ClusterPicker is distributed in the hope that it will be useful, 21 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 22 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 23 | * GNU General Public License for more details. 24 | * 25 | * You should have received a copy of the GNU General Public License 26 | * along with ClusterPicker. If not, see . 27 | * 28 | * 29 | * @author Samantha Lycett 30 | * @created 21 Sept 2011 31 | * @version 21 Sept 2011 32 | * @version 22 Sept 2011 - test 5 33 | */ 34 | public class TreeTester { 35 | 36 | public static void test1() { 37 | 38 | System.out.println("** Test 1 - define a tree from a newick string"); 39 | 40 | String trLine = "(A:1,B:2)0.9:1"; 41 | 42 | System.out.println("Newick tree line = "+trLine); 43 | 44 | System.out.println("Create tree .... "); 45 | Tree t = new Tree(); 46 | t.readTree(trLine); 47 | 48 | System.out.println("Node details"); 49 | System.out.println(t.nodesInfo()); 50 | 51 | } 52 | 53 | public static void test2() { 54 | 55 | System.out.println("** Test 2 - read in a tree from file and print out the node details"); 56 | 57 | String filename = "C://Users//Samantha Lycett//Documents//Emma//ARefFT5.9.newick"; 58 | //String filename = "C://Users//Samantha Lycett//Documents//Emma//example.nwk"; 59 | TreeReader inT = new TreeReader(); 60 | inT.setFileName(filename); 61 | inT.openFile(); 62 | Tree t = inT.readNextTree(); 63 | inT.closeFile(); 64 | 65 | System.out.println(t.nodesInfo()); 66 | 67 | } 68 | 69 | public static void test3() { 70 | 71 | System.out.println("** Test 3 - read in a tree from file and print out a few node details, including MRCA function"); 72 | 73 | String filename = "C://Users//Samantha Lycett//Documents//Emma//ARefFT5.9.newick"; 74 | //String filename = "C://Users//Samantha Lycett//Documents//Emma//example.nwk"; 75 | TreeReader inT = new TreeReader(); 76 | inT.setFileName(filename); 77 | inT.openFile(); 78 | Tree t = inT.readNextTree(); 79 | inT.closeFile(); 80 | 81 | Node a = t.getNode("124153"); //t.getNode("122109"); 82 | Node b = t.getNode("Node143"); //t.getNode("Node539"); 83 | Node c = t.MRCA(a, b); 84 | 85 | System.out.println("Chosen Node 1"); 86 | System.out.println(a.info()); 87 | 88 | System.out.println("Chosen Node 2"); 89 | System.out.println(b.info()); 90 | 91 | System.out.println("MRCA of Node 1 & 2"); 92 | System.out.println(c.info()); 93 | 94 | System.out.println("All children info for "+c.getName()); 95 | for (Node dd : c.getAllMyChildren() ) { 96 | System.out.println(dd.info()); 97 | } 98 | 99 | System.out.println("Test newick string writing from nodes (to screen)"); 100 | System.out.println(a.toString()); 101 | System.out.println(b.toString()); 102 | System.out.println(c.toString()); 103 | 104 | System.out.println("Number of progeny (tips) for "+c.getName()); 105 | System.out.println(c.calcNumProgeny()); 106 | 107 | } 108 | 109 | public static void test4() { 110 | 111 | System.out.println("** Test 4 - Read in Tree from File, extract subtree from a particular node, and write subtree to file"); 112 | 113 | String filename = "C://Users//Samantha Lycett//Documents//Emma//ARefFT5.9.newick"; 114 | //String filename = "C://Users//Samantha Lycett//Documents//Emma//example.nwk"; 115 | TreeReader inT = new TreeReader(); 116 | inT.setFileName(filename); 117 | inT.openFile(); 118 | Tree t = inT.readNextTree(); 119 | inT.closeFile(); 120 | 121 | Node a = t.getNode("Node539"); 122 | Node r = t.getRoot(); 123 | 124 | System.out.println("Number of progeny for "+r.getName()+" = "+r.calcNumProgeny()); 125 | System.out.println("Number of progeny for "+a.getName()+" = "+a.getNumberProgeny()); 126 | 127 | Tree ta = t.subTree(a); 128 | Node ra = ta.getRoot(); 129 | 130 | System.out.println("List of tips for "+ra.getName()); 131 | System.out.println(ta.tipList()); 132 | 133 | System.out.println("Root node info for subtree from "+ra.getName()); 134 | System.out.println(ra.info()); 135 | 136 | 137 | try { 138 | BufferedWriter outFile = new BufferedWriter(new FileWriter("C://Users//Samantha Lycett//Documents//Emma//example_rootNode.nwk")); 139 | outFile.write(r.toString()+";"); 140 | outFile.newLine(); 141 | outFile.close(); 142 | 143 | BufferedWriter outFile2 = new BufferedWriter(new FileWriter("C://Users//Samantha Lycett//Documents//Emma//example_subTree.nwk")); 144 | outFile2.write(ta.toString()+";"); 145 | outFile2.newLine(); 146 | outFile2.close(); 147 | 148 | } catch (IOException e) { 149 | System.out.println(e.toString()); 150 | } 151 | 152 | 153 | } 154 | 155 | public static void test5() { 156 | System.out.println("** Test 5 - read tree from file, split into subtrees with good support"); 157 | 158 | String filename = "C://Users//Samantha Lycett//Documents//Emma//ARefFT5.9.newick"; 159 | //String filename = "C://Users//Samantha Lycett//Documents//Emma//example.nwk"; 160 | TreeReader inT = new TreeReader(); 161 | inT.setFileName(filename); 162 | inT.openFile(); 163 | Tree t = inT.readNextTree(); 164 | inT.closeFile(); 165 | 166 | double supportThres = 0.95; 167 | List subTrs = t.subTrees_with_support(supportThres); 168 | 169 | System.out.println("Number of subtrees with support >= "+supportThres+" = "+subTrs.size()); 170 | for (Tree st : subTrs) { 171 | System.out.println(st.toString()); 172 | } 173 | 174 | 175 | String outName = filename.replace(".newick", "_subtrees.nwk"); 176 | System.out.println("Writing subtrees to "+outName); 177 | TreeWriter outFile = new TreeWriter(); 178 | outFile.write(subTrs, outName); 179 | } 180 | 181 | public static void test6() { 182 | System.out.println("** Cluster Picker Test "); 183 | 184 | //String sequencesName = "C://Users//Samantha Lycett//Documents//Emma//B_outgroup_refSeq.fas"; //A_outgroup_refSeq.fas"; 185 | //String treeName = "C://Users//Samantha Lycett//Documents//Emma//BRefFT5.4.newick"; //ARefFT5.9.newick"; 186 | String sequencesName = "C://Users//Samantha Lycett//Documents//Emma//C_outgroup_refSeq.fas"; //A_outgroup_refSeq.fas"; 187 | String treeName = "C://Users//Samantha Lycett//Documents//Emma//CRefFT5.11.newick"; //ARefFT5.9.newick"; 188 | 189 | //BasicSequence.useAbs = false; 190 | BasicSequence.differenceType = "gap"; 191 | 192 | ClusterPicker cp = new ClusterPicker(); 193 | cp.setInitialSupportThres(0.95); 194 | cp.setSupportThres(0.9); 195 | cp.setGeneticThres(4.5/100); 196 | cp.readSequences(sequencesName); 197 | cp.readTree(treeName); 198 | cp.processData(); 199 | cp.writeResults(); 200 | 201 | } 202 | 203 | public static void test7() { 204 | System.out.println("** Cluster Picker Test on 5 data sets **"); 205 | 206 | ClusterPicker.test(); 207 | 208 | } 209 | 210 | public static void testBEASTTree() { 211 | 212 | System.out.println("** Test Cluster Picking on BEAST Tree -> NWK only **"); 213 | 214 | String path = "C://data//human_flu//epidemics3//scottish//clades//"; 215 | String name = "genomes_492_GTR_GI4_strict_exponentialGrowth_expPriors_4.combined.tre.posterior.1.nwk"; 216 | 217 | //String treeName = "C://data//human_swine_flu_sanger_sequencing//final_sequences//phrap_assemblies_15Nov2010_with_alb_mod//clades//genomes_492_GTR_GI4_strict_exponentialGrowth_expPriors_4.combined.posterior.nwk"; 218 | String treeName = path + name; 219 | String outName = treeName.replace(".nwk", "") + "_clusters_withSupport.figTree"; 220 | 221 | double supportThres = 0.5; 222 | 223 | // read tree 224 | Tree theTree = (new TreeReader()).readTree(treeName); 225 | System.out.println("Read tree with "+theTree.tipNames().size()+" tips"); 226 | 227 | // break to supported subtrees 228 | List subTrees = theTree.subTrees_with_support(supportThres); 229 | System.out.println("Found "+subTrees.size()+" subTrees"); 230 | 231 | // initialise output file (figTree) 232 | FigTreeWriter figTree = new FigTreeWriter(); 233 | figTree.loadRainbowColours(); 234 | 235 | // rename tips according to cluster 236 | int clusterNumber = 0; 237 | Hashtable clusteredSequenceNames = new Hashtable(); 238 | 239 | for (Tree st : subTrees) { 240 | clusterNumber++; 241 | 242 | for (String tipName : st.tipNames()) { 243 | String newName = "Clust"+clusterNumber+"_"+tipName; 244 | clusteredSequenceNames.put(tipName, newName); 245 | 246 | int col = (int)Math.floor((double)(255*clusterNumber)/(double)subTrees.size()); 247 | figTree.setColour(newName, col); 248 | 249 | System.out.println(tipName+"\t"+newName+"\t"+col); 250 | } 251 | 252 | } 253 | 254 | for (Node n : theTree.getNodes()) { 255 | if ( clusteredSequenceNames.containsKey(n.getName() ) ) { 256 | String newName = clusteredSequenceNames.get(n.getName()); 257 | n.setName(newName); 258 | } 259 | } 260 | 261 | figTree.writeTree(theTree, outName); 262 | 263 | } 264 | 265 | public static void test8() { 266 | System.out.println("** Cluster Picker Test on BEAST Tree -> NWK only **"); 267 | 268 | String path = "C://data//human_flu//epidemics3//scottish//clades//"; 269 | String name = "genomes_492"; 270 | 271 | //String treeName = path + name + "_GTR_GI4_strict_exponentialGrowth_expPriors_4.combined.tre.posterior.1.nwk"; 272 | String treeName = path + name + "_beast_mcc.nwk"; 273 | 274 | double initialSupportThres = 0.5; 275 | double supportThres = 0.5; 276 | double geneticThres = 4.5/100; 277 | 278 | String sequencesName = path + name + ".fas"; 279 | 280 | 281 | //BasicSequence.useAbs = false; 282 | //BasicSequence.differenceType = "gap"; 283 | 284 | ClusterPicker cp = new ClusterPicker(); 285 | cp.setInitialSupportThres(initialSupportThres); 286 | cp.setSupportThres(supportThres); 287 | cp.setGeneticThres(geneticThres); 288 | cp.readSequences(sequencesName); 289 | cp.readTree(treeName); 290 | cp.processData(); 291 | cp.writeResults(); 292 | 293 | } 294 | 295 | public static void main (String args[]) { 296 | System.out.println("** Trees Tester **"); 297 | //test1(); 298 | //test2(); 299 | //test3(); 300 | //test4(); 301 | //test5(); 302 | //test6(); 303 | //test7(); 304 | 305 | //testBEASTTree(); 306 | test8(); 307 | 308 | System.out.println("** END **"); 309 | } 310 | 311 | } 312 | -------------------------------------------------------------------------------- /src/clusterPicking/TreeWriter.java: -------------------------------------------------------------------------------- 1 | package clusterPicking; 2 | 3 | import java.io.*; 4 | import java.util.List; 5 | 6 | /** 7 | * class to write newick tree strings to file 8 | * Copyright (C) 2013 Samantha Lycett 9 | * 10 | * This file is part of ClusterPicker. 11 | * 12 | * ClusterPicker is free software: you can redistribute it and/or modify 13 | * it under the terms of the GNU General Public License as published by 14 | * the Free Software Foundation, either version 3 of the License, or 15 | * any later version. 16 | * 17 | * ClusterPicker is distributed in the hope that it will be useful, 18 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 19 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 20 | * GNU General Public License for more details. 21 | * 22 | * You should have received a copy of the GNU General Public License 23 | * along with ClusterPicker. If not, see . 24 | * 25 | * 26 | * @author Samantha Lycett 27 | * @created 22 Sept 2011 28 | * @version 22 Sept 2011 29 | */ 30 | public class TreeWriter { 31 | 32 | private String filename; 33 | private BufferedWriter outFile; 34 | private boolean open = false; 35 | 36 | public TreeWriter() { 37 | Node.setFigTreeFormat(false); 38 | } 39 | 40 | /////////////////////////////////////////////////////////////////////////////////////////// 41 | 42 | public void setFilename(String fn) { 43 | this.filename = fn; 44 | } 45 | 46 | ///////////////////////////////////////////////////////////////////////////////////////// 47 | 48 | public void openFile(String fn) { 49 | this.filename = fn; 50 | openFile(); 51 | } 52 | 53 | public void openFile() { 54 | try { 55 | outFile = new BufferedWriter(new FileWriter(filename)); 56 | open = true; 57 | } catch (IOException e) { 58 | System.out.println(e.toString()); 59 | } 60 | } 61 | 62 | /** 63 | * appends the newick string of Tree t to file - note the file must be already open 64 | * allows multiple tree lines to be written to file 65 | * @param t 66 | */ 67 | public void append(Tree t) { 68 | if (open) { 69 | try { 70 | outFile.write(t.toString()+";"); 71 | outFile.newLine(); 72 | } catch (IOException e) { 73 | System.out.println(e.toString()); 74 | } 75 | } else { 76 | System.out.println("TreeWriter:append WARNING: nothing has been written because the file is not open for appending"); 77 | } 78 | } 79 | 80 | public void closeFile() { 81 | if (open) { 82 | try { 83 | outFile.close(); 84 | open = false; 85 | } catch (IOException e) { 86 | System.out.println(e.toString()); 87 | } 88 | } 89 | } 90 | 91 | //////////////////////////////////////////////////////////////////////////////////////// 92 | 93 | /** 94 | * writes the newick string from input Tree t to filename and closes the file. 95 | * use this method to write a single tree to a single file 96 | * @param t 97 | * @param filename 98 | */ 99 | public void write(Tree t, String filename) { 100 | try { 101 | BufferedWriter outFile = new BufferedWriter(new FileWriter(filename)); 102 | outFile.write(t.toString()+";"); 103 | outFile.newLine(); 104 | outFile.close(); 105 | } catch (IOException e) { 106 | System.out.println(e.toString()); 107 | } 108 | } 109 | 110 | /** 111 | * writes the set of newick strings from the input Tree list to filename, and closes the file 112 | * @param ts 113 | * @param filename 114 | */ 115 | public void write(List ts, String filename) { 116 | this.filename=filename; 117 | openFile(); 118 | for (Tree t : ts) { 119 | append(t); 120 | } 121 | closeFile(); 122 | } 123 | 124 | } 125 | -------------------------------------------------------------------------------- /src/clusterPicking/WriteFasta.java: -------------------------------------------------------------------------------- 1 | package clusterPicking; 2 | 3 | import java.io.*; 4 | import java.util.*; 5 | 6 | /** 7 | * class to write fasta format files 8 | * Copyright (C) 2013 Samantha Lycett 9 | * 10 | * This file is part of ClusterPicker. 11 | * 12 | * ClusterPicker is free software: you can redistribute it and/or modify 13 | * it under the terms of the GNU General Public License as published by 14 | * the Free Software Foundation, either version 3 of the License, or 15 | * any later version. 16 | * 17 | * ClusterPicker is distributed in the hope that it will be useful, 18 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 19 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 20 | * GNU General Public License for more details. 21 | * 22 | * You should have received a copy of the GNU General Public License 23 | * along with ClusterPicker. If not, see . 24 | * 25 | * 26 | * @author Samantha Lycett 27 | * @created 23 Sept 2011 28 | * @version 23 Sept 2011 29 | */ 30 | public class WriteFasta { 31 | 32 | private String fileName; 33 | private BufferedWriter outFile; 34 | private boolean open = false; 35 | private String fastaStart = ">"; 36 | 37 | public WriteFasta() { 38 | 39 | } 40 | 41 | /////////////////////////////////////////////////////////////////////////////////////// 42 | 43 | public void openFile() { 44 | try { 45 | outFile = new BufferedWriter(new FileWriter(fileName)); 46 | open = true; 47 | } catch (IOException e) { 48 | System.out.println(e.toString()); 49 | } 50 | } 51 | 52 | public void openFile(String fileName) { 53 | this.fileName = fileName; 54 | openFile(); 55 | } 56 | 57 | public void closeFile() { 58 | if ( open ) { 59 | try { 60 | open = false; 61 | outFile.close(); 62 | } catch (IOException e) { 63 | System.out.println(e.toString()); 64 | } 65 | } 66 | } 67 | 68 | 69 | public void append(String sequenceName, String sequence) { 70 | if (open) { 71 | try { 72 | 73 | if (sequenceName.startsWith(fastaStart)) { 74 | outFile.write(sequenceName); 75 | } else { 76 | outFile.write(fastaStart+sequenceName); 77 | } 78 | outFile.newLine(); 79 | outFile.write(sequence); 80 | outFile.newLine(); 81 | 82 | } catch (IOException e) { 83 | System.out.println(e.toString()); 84 | } 85 | } else { 86 | System.out.println("WriteFasta:append WARNING - file is not open, nothing was written"); 87 | } 88 | } 89 | 90 | public void append(BasicSequence s) { 91 | if (open) { 92 | try { 93 | String sequenceName = fastaStart + s.header(); 94 | outFile.write(sequenceName); 95 | outFile.newLine(); 96 | 97 | String sequence = new String( s.charSeq() ); 98 | outFile.write(sequence); 99 | outFile.newLine(); 100 | } catch (IOException e) { 101 | System.out.println(e.toString()); 102 | } 103 | } else { 104 | System.out.println("WriteFasta:append WARNING - file is not open, nothing was written"); 105 | } 106 | } 107 | 108 | public void append(List seqs) { 109 | if (open) { 110 | try { 111 | for (BasicSequence s : seqs) { 112 | String sequenceName = fastaStart + s.header(); 113 | outFile.write(sequenceName); 114 | outFile.newLine(); 115 | 116 | String sequence = new String( s.charSeq() ); 117 | outFile.write(sequence); 118 | outFile.newLine(); 119 | } 120 | } catch (IOException e) { 121 | System.out.println(e.toString()); 122 | } 123 | } else { 124 | System.out.println("WriteFasta:append WARNING - file is not open, nothing was written"); 125 | } 126 | } 127 | 128 | } 129 | -------------------------------------------------------------------------------- /src/clusterPicking/rainbow_256_cols.java: -------------------------------------------------------------------------------- 1 | package clusterPicking; 2 | 3 | import java.util.ArrayList; 4 | import java.util.Arrays; 5 | import java.util.List; 6 | 7 | /** 8 | * class to represent rainbow colours; 256 values 9 | * this was put in here to make the jar file export easier (rather than as a separate file as in early versions) 10 | * Copyright (C) 2013 Samantha Lycett 11 | * 12 | * This file is part of ClusterPicker. 13 | * 14 | * ClusterPicker is free software: you can redistribute it and/or modify 15 | * it under the terms of the GNU General Public License as published by 16 | * the Free Software Foundation, either version 3 of the License, or 17 | * any later version. 18 | * 19 | * ClusterPicker is distributed in the hope that it will be useful, 20 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 21 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 22 | * GNU General Public License for more details. 23 | * 24 | * You should have received a copy of the GNU General Public License 25 | * along with ClusterPicker. If not, see . 26 | * 27 | * 28 | * @author Samantha Lycett 29 | * @created 27 March 2012 30 | * @vesrion 27 March 2012 31 | */ 32 | public class rainbow_256_cols { 33 | 34 | private static String[] cols = 35 | { 36 | "#FF0000", 37 | "#FF0600", 38 | "#FF0C00", 39 | "#FF1200", 40 | "#FF1800", 41 | "#FF1E00", 42 | "#FF2400", 43 | "#FF2A00", 44 | "#FF3000", 45 | "#FF3600", 46 | "#FF3C00", 47 | "#FF4200", 48 | "#FF4800", 49 | "#FF4E00", 50 | "#FF5400", 51 | "#FF5A00", 52 | "#FF6000", 53 | "#FF6600", 54 | "#FF6C00", 55 | "#FF7200", 56 | "#FF7800", 57 | "#FF7E00", 58 | "#FF8300", 59 | "#FF8900", 60 | "#FF8F00", 61 | "#FF9500", 62 | "#FF9B00", 63 | "#FFA100", 64 | "#FFA700", 65 | "#FFAD00", 66 | "#FFB300", 67 | "#FFB900", 68 | "#FFBF00", 69 | "#FFC500", 70 | "#FFCB00", 71 | "#FFD100", 72 | "#FFD700", 73 | "#FFDD00", 74 | "#FFE300", 75 | "#FFE900", 76 | "#FFEF00", 77 | "#FFF500", 78 | "#FFFB00", 79 | "#FDFF00", 80 | "#F7FF00", 81 | "#F1FF00", 82 | "#EBFF00", 83 | "#E5FF00", 84 | "#DFFF00", 85 | "#D9FF00", 86 | "#D3FF00", 87 | "#CDFF00", 88 | "#C7FF00", 89 | "#C1FF00", 90 | "#BBFF00", 91 | "#B5FF00", 92 | "#AFFF00", 93 | "#A9FF00", 94 | "#A3FF00", 95 | "#9DFF00", 96 | "#97FF00", 97 | "#91FF00", 98 | "#8BFF00", 99 | "#85FF00", 100 | "#80FF00", 101 | "#7AFF00", 102 | "#74FF00", 103 | "#6EFF00", 104 | "#68FF00", 105 | "#62FF00", 106 | "#5CFF00", 107 | "#56FF00", 108 | "#50FF00", 109 | "#4AFF00", 110 | "#44FF00", 111 | "#3EFF00", 112 | "#38FF00", 113 | "#32FF00", 114 | "#2CFF00", 115 | "#26FF00", 116 | "#20FF00", 117 | "#1AFF00", 118 | "#14FF00", 119 | "#0EFF00", 120 | "#08FF00", 121 | "#02FF00", 122 | "#00FF04", 123 | "#00FF0A", 124 | "#00FF10", 125 | "#00FF16", 126 | "#00FF1C", 127 | "#00FF22", 128 | "#00FF28", 129 | "#00FF2E", 130 | "#00FF34", 131 | "#00FF3A", 132 | "#00FF40", 133 | "#00FF46", 134 | "#00FF4C", 135 | "#00FF52", 136 | "#00FF58", 137 | "#00FF5E", 138 | "#00FF64", 139 | "#00FF6A", 140 | "#00FF70", 141 | "#00FF76", 142 | "#00FF7C", 143 | "#00FF81", 144 | "#00FF87", 145 | "#00FF8D", 146 | "#00FF93", 147 | "#00FF99", 148 | "#00FF9F", 149 | "#00FFA5", 150 | "#00FFAB", 151 | "#00FFB1", 152 | "#00FFB7", 153 | "#00FFBD", 154 | "#00FFC3", 155 | "#00FFC9", 156 | "#00FFCF", 157 | "#00FFD5", 158 | "#00FFDB", 159 | "#00FFE1", 160 | "#00FFE7", 161 | "#00FFED", 162 | "#00FFF3", 163 | "#00FFF9", 164 | "#00FFFF", 165 | "#00F9FF", 166 | "#00F3FF", 167 | "#00EDFF", 168 | "#00E7FF", 169 | "#00E1FF", 170 | "#00DBFF", 171 | "#00D5FF", 172 | "#00CFFF", 173 | "#00C9FF", 174 | "#00C3FF", 175 | "#00BDFF", 176 | "#00B7FF", 177 | "#00B1FF", 178 | "#00ABFF", 179 | "#00A5FF", 180 | "#009FFF", 181 | "#0099FF", 182 | "#0093FF", 183 | "#008DFF", 184 | "#0087FF", 185 | "#0081FF", 186 | "#007CFF", 187 | "#0076FF", 188 | "#0070FF", 189 | "#006AFF", 190 | "#0064FF", 191 | "#005EFF", 192 | "#0058FF", 193 | "#0052FF", 194 | "#004CFF", 195 | "#0046FF", 196 | "#0040FF", 197 | "#003AFF", 198 | "#0034FF", 199 | "#002EFF", 200 | "#0028FF", 201 | "#0022FF", 202 | "#001CFF", 203 | "#0016FF", 204 | "#0010FF", 205 | "#000AFF", 206 | "#0004FF", 207 | "#0200FF", 208 | "#0800FF", 209 | "#0E00FF", 210 | "#1400FF", 211 | "#1A00FF", 212 | "#2000FF", 213 | "#2600FF", 214 | "#2C00FF", 215 | "#3200FF", 216 | "#3800FF", 217 | "#3E00FF", 218 | "#4400FF", 219 | "#4A00FF", 220 | "#5000FF", 221 | "#5600FF", 222 | "#5C00FF", 223 | "#6200FF", 224 | "#6800FF", 225 | "#6E00FF", 226 | "#7400FF", 227 | "#7A00FF", 228 | "#8000FF", 229 | "#8500FF", 230 | "#8B00FF", 231 | "#9100FF", 232 | "#9700FF", 233 | "#9D00FF", 234 | "#A300FF", 235 | "#A900FF", 236 | "#AF00FF", 237 | "#B500FF", 238 | "#BB00FF", 239 | "#C100FF", 240 | "#C700FF", 241 | "#CD00FF", 242 | "#D300FF", 243 | "#D900FF", 244 | "#DF00FF", 245 | "#E500FF", 246 | "#EB00FF", 247 | "#F100FF", 248 | "#F700FF", 249 | "#FD00FF", 250 | "#FF00FB", 251 | "#FF00F5", 252 | "#FF00EF", 253 | "#FF00E9", 254 | "#FF00E3", 255 | "#FF00DD", 256 | "#FF00D7", 257 | "#FF00D1", 258 | "#FF00CB", 259 | "#FF00C5", 260 | "#FF00BF", 261 | "#FF00B9", 262 | "#FF00B3", 263 | "#FF00AD", 264 | "#FF00A7", 265 | "#FF00A1", 266 | "#FF009B", 267 | "#FF0095", 268 | "#FF008F", 269 | "#FF0089", 270 | "#FF0083", 271 | "#FF007E", 272 | "#FF0078", 273 | "#FF0072", 274 | "#FF006C", 275 | "#FF0066", 276 | "#FF0060", 277 | "#FF005A", 278 | "#FF0054", 279 | "#FF004E", 280 | "#FF0048", 281 | "#FF0042", 282 | "#FF003C", 283 | "#FF0036", 284 | "#FF0030", 285 | "#FF002A", 286 | "#FF0024", 287 | "#FF001E", 288 | "#FF0018", 289 | "#FF0012", 290 | "#FF000C", 291 | "#FF0006" }; 292 | 293 | public static List getRainbowColours() { 294 | 295 | List rainbowCols = new ArrayList(); 296 | rainbowCols.addAll(Arrays.asList(cols)); 297 | 298 | return rainbowCols; 299 | } 300 | 301 | 302 | } 303 | --------------------------------------------------------------------------------