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Example with Starting State
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#NEXUS Begin data; Dimensions ntax=3 nchar=500; Format datatype=dna symbols="ACTG" missing=? gap=-; Matrix [0, 500] A TCGCGCTAACGTCGTTTATAAGTGATCAAAGATAAAAGGAAATCTAAGCTGCCTTCATGTTCCTCATCGGACCTGCACAAGGATGGGCGTGGAGATTCTGGCATGGATACTGTACTTTTACGCGATCGCCCCAGCTACCGACCTCTATAATCACAGGGAATCTCGGGGAACGAATTGCTTCACTAGGTCACACCCGGTTTATAGCCCGTAGAAGTTAGAGCCCGCGAATAAAGGACTAACAACTCTTATCAAGCTAAGGGACATCCTAGAGGGACCTCTGCGGGAGCAGCATGTTGTGTGACTCATCACGGTAAGAACTTGGCAAGCGCGACAGCGGCTAAGCCAGCATGCTAGGCGTCGTCGGATAGTCGCCGTCACGGAATCGGATGAGATCCCTTGAGGGATTGATGATGTTCACATCACTACATGGTTGTTCTGAGTGTTGGTGATCAGGTGCAGCAATTGTGCTTGACGGAAATGGGCTCTCATAACCGAACCCA C GCGCACCTCCCTCGGATATAAGTGACCGAAGAGAAAAGGGAATCTAATTGGCCCTATCATCACTCATCGTACCTGATCACGTATGGCTGTGGAGATTGCGGCATGGATACTGTACTTTTGAGCGATCATCCCAGTTACCGACCTTCTTAATAAGAGGGAACCTAGGGTAAAGGAATGCTCCACTCCGTCACACGGGGTATATATCCGGAATATGTTAGGCCCCCCGAATGAAGGAGTAAAAACTCTTAACAAGCTCCGACAGATCCTAGGGTATCGTCTGCGGGGCCGGCAGGTCGTGGGACGCATCACGCTAAACACTTGGCAAGCGTGACAGCGGCTGGGTCAGAATGCTCGGCCACGCCGTTTAGTCGCCGGCACCGAATCGAATGTGATCCCTTGAGGAAATGATGAAGTTAACATCATTACATGGGTGCTCTGAGTGATGGTGATAAGGTGGAGGACTTGTGTTTGACGGAAATGGGCTCTGAAAACCGAACTCT B GCGCACCTACTGCGGATATAAGTGACCGAAGAGTAATGGGAATCTATGCGGCCCTCGCGTCTCTCATCGTACCTGATCAAGTATGGGCGTGGAGATTGTGGCATGGATACTGTACTTTTGAGCCATCATCCCAGTTACCGACCTTCGTAATAAGAGCGAGCCTAGGGGAAAGAAATGCTCCACTCCATCACACCGGGTATATATCCGGAATATGTTCGAGCCCCCGAATAAAGGAGTAAAAACTCTTAACAAGCTCCGAAACATCCTAGGGTATCCTCTGCAGGGACGGCATGTTGTGGGGCCCATCACCCTAAGACCTTTGCAAGCATGAAAGCGGCTCAGCCAGCATGCTCGATCCCGCCGTACAGTCGCCGGCACGGAATCGAGTGTGATCCCCTGAGGAATTGATGAAGTTAACATCACTACTTGGCTGCTCTGAGTGCTGGTGATCAGGTGCAGCACATATGTGTGACGGAAATGGGCACTGACAACCGAACTAT [1, 500] A GAAACGGATCTAAGTGTACGGTTTCTCTCGAAGGGGGCACCTTTGCTATGCCCACCCCCATCTTGGAAGTGCGAGACCATACTCGCGCGTGCGTCAGGTTCTTACTTGATTTCGGCGGGGGTGGCTAAATTTTAGCTAGGGATCTAGAAATCCGTCATAGTCCTACAGGGCCATTCTGCCGCTTGCTAGCGTTGGTGATACGAGGGCAACTTTGAACTTTACGCGGAACTCCCCACCTCAGAGACTGTTACGACGTAGGCTAAATGTGCCGTGATTTCTGAGGGCAAAAGCCGTGCAAGGATGGACGGGGGTGCTCAAACAACTGCATCAGCCTCGGCATTATCTTGCATGAGCGCCTTCGATCGGTCACCAGTCGGCTAGATTACAAGCAAGCTCTTCGGAGGAGATGAGCTCGCATGGATCACGCGTCTACGTAACTTTCAGGGTCCATCCAAATGTCAATCATTCACCGAATGGCGATCGTCAGGTACGCGATTCCA C CGCTCGGATCTAAGTGTACGGTTTCTCTCGAAGGTGGAACCATTGCTATACCCACCCCCATCTTGGAAGTGCCAAACCATTCTCCCAAGAGCGTCGGGTTCTTACTCGATTTCGGCGGGGGTGGCTACAATTTAGGTAGGGATCTAGAAATCGGTTATAATCCTACAAAGCCATTCTGGCGCTTGCTAGTGTTGGTGATACGAGGGCAGCTTTGAACTTTACCGGGAACTGGGCACCTAAGGGACTGTGTCGACGTAGGCTAAATGTGCCGTGATTTCAGCGAGCAAAAGCCATGCAAGATTGGACGGGGGGCCTCAAACAACTGCATCAGCCTCGATATTATCTTGCATGAGCTCCTTCGATCGGTTCCCAGTCGGCTATATTATAAGCAAGCTCTTCGGAGGATATGAGCACGCACGGATTCCGCGTCTACGTAACTTTGAGGGCCCAGCCAGCAGTCAATCATTCAACGAATGGCGATCATAACGAACGCGATTCCA B CGCTCGGATCTAAGTGTACGGTTTCTCTGGAAGGTGGAACCATTGCTATACCCATCCCCATCTTGGAAGTGCCAGACCATTCTCCCAAGAGCGTCTGGTTCTTACTCGATTTCGGCGGGGGTGGCTACAATTTAGGTAGGGATCTAGAAATCGGTGATAATCGTACAAAGCCATTCTGGCGCTTGCTAGTGTCGGTGATACGAGAGCAGCTTTGAACTTTACCCGGAACTGCGCACCTAAGGGACTGTGTCGACGTAGGCTAAATGTGCCGTGATTTCAGCGAGCAAAAGCCATGCAAGATTGGACGGGCGGCCTCAAACAACTGCATCAGCCTCGATATTATCTTGCATGAGCTCCTTCGATCGGTTCCCAGTCGGCTATCTTATAAGCAAGCTCTTCGGAGGATATGAGCACGCACGGATTCCGCGTCTACGTAACTTTGAGGGCCCAGCCAGCAGTCAATCATTGACCGAATGGCGATCATAACGAACGCGATTCCA ;End; BEGIN TREES; Tree gt0 = (A:0.119900443,(C:0.058838639,B:0.058838639):0.061061803); Tree gt1 = (A:0.068766378,(C:0.016229589,B:0.016229589):0.052536789); END; BEGIN NETWORKS; Network net1 = (((B:0.0)I3#H1:0.05::0.8,(C:2.0E-8,I3#H1:2.0E-8::0.2)I2:0.04999998)I1:0.01,A:0.06)I0; END; BEGIN PHYLONET; MCMC_SEQ -cl 50000 -bl 10000 -sgt (gt0,gt1) -snet net1 -sps 0.04 -pre 20; END; |
Example given Missing Data
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#NEXUS Begin data; Dimensions ntax=5 nchar=108; Format datatype=dna symbols="ACTG" missing=? gap=-; Matrix [loci1, 53, ...] a1 ATTGGAGACRAGCGARGACCGAGCTCACGAACCTGAGGAATGGAATCGATTAC a2 ATTTGAGACRAGCGARGACCGAGCTCACGAACCTGAGGANTGGAATCGATTAC b1 TTGGGAGACGAGCGAAGACAGAGCATATGAGCCTAAGGATTGGAATCGATTGT b2 TTGGGAGACGAGCGAAGACAGAGCATATGAGCCTGAGGATTGGAATCGATTGT [loci2, 58, ...] a2 ACTTTGCAAGCCAAAAATGGTATGCGAGACAACGCCTGTCATGGATGATGAACCAGAT b1 GCTTTGCAAGCCTAAGATGGTTTGCGAGACGACGATGGCAGTCGACGATGAATCAGAC b2 GCTTTGCAAGCCTAAGATGGTTTGCGAGACGACGATGGCAGTCGACGATGAATCAGAC c1 GCTTTGRAAGRCAAAAATGATATGCGAAACAACGCCCGTGATGGACGATGAACAGGAT ;End; BEGIN PHYLONET; MCMC_SEQ -loci (loci1,loci2) -cl 5000000 -bl 1000000 -tm <A:a1,a2; B:b1,b2; C:c1>; END; |
Understanding the Output
System Output
- Logger: each time a sample is collected, the program prints out the Posterior value, current ESS (Effective Sample Size) based on the posterior values, likelihood value, prior value, current ESS based on the prior values, and the sampled phylogenetic network. Note the value in the brackets is the population size.
- Summarization: the program prints out the chain length, burn-in length, sample frequency and the overall acceptance rate of proposals.
- Operations: the usage and the acceptance rate for each operation.
- Topologies: the MAP (Maximum A Posterior) topology is given. For each unique topology, the network with the maximum posterior value and the averaged (branch lengths and inheritance probabilities) network are printed out. The topologies are ranked on their posterior probabilities.
- Run time: the elapsed time.
MCMC_SEQ -cl 250000 -bl 50000 -sf 5000 ----------------------- Logger: ----------------------- Overall MAP = -139.6655535361708 (((Spar:0.054401097303896875,Scer:0.054401097303896875):0.02940261095452569,Smik:0.08380370825842257):0.015640290731517764,(Sbay:0.038489186677349164,Skud:0.038489186677349164):0.060954812312591165); Total elapsed time : 27.35100 s |
Sample Files
The phylogenetic network, gene trees and the hyper-parameter of the population size are logged into files under your home directory or the directory specified by "-dir outDirectory".
- Phylogenetic Network: ~/outDirectory/network.log
- Hyper-parameter of Population size: ~/outDirectory/popSizePrior.log
- Gene tree: ~/outDirectory/tree_locusName.log
Downloads
- example.zip
- example.nexus: input file for PhyloNet
- example.txt: system output
- network.log, popSizePrior.log, tree_YAL053W.log, tree_YAR007C.log, tree_YBL015W.log: sample files
- The yeast data set (Rokas et al., 2003) sampled from seven Saccharomyces species S. cerevisiae (Scer), S. paradoxus (Spar), S. mikatae (Smik), S. kudriavzevii (Skud), S. bayanus (Sbay), S. castellii (Scas) and S. kluyveri (Sklu)
- The wheat data set (Marcussen et al., 2014) sampled from hexaploid bread wheat subgenomes T. aestivum TaA (A subgenome), TaB (B subgenome) and TaD (D subgenome), and five diploid relatives T. monococcum (Tm), T. urartu (Tu), Ae. sharonensis (Ash), Ae. speltoides (Asp) and Ae. tauschii (At)
- The mosquito data set (Fontaine et al., 2014) sampled from six Anopheles species An. gambiae (G), An. coluzzii (C), An. arabiensis (A), An. quadriannulatus (Q), An. merus (R) and An. melas (L)
Command References
- D.Wen and L. Nakhleh. Co-estimating reticulate phylogenies and gene trees on sequences from multiple independent loci. Submitted.
- Gronau, Ilan, et al. Bayesian inference of ancient human demography from individual genome sequences. Nature genetics 43.10 (2011): 1031-1034.