Versions Compared

Old Version 56

changes.mady.by.user Ellie Wen

Saved on

compared with

New Version 57

changes.mady.by.user Ellie Wen

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  • Co-estimation of reticulate phylogenies (ILS & hybridization) and , gene trees, divergence times and population sizes on sequences from multiple independent loci.

    Usage

     

    MCMC

    Usage

     

    MCMC_SEQ -loci locusList [-cl chainLength] [-bl burnInLength] [-sf sampleFrequency] [-sd seed] [-pl parallelThreads] [-dir outDirectory] [-mc3 temperatureList] [-mr maxReticulation] [-tm taxonMap] [-fixps popSize] [-varyps] [-pp poissonParameter] [-dd] [-ee] [-sgt startingGeneTrees] [-snet startingNetwork] [-sps startingPopSize] [-pre preBurnIn] [-gtr paramList] [-diploid diploidSpeciesList]



    MCMC Settings
    -loci locusListThe list of loci used in the inference. For example, -loci (YNR008W,YNL313C) indicates the inference is performed on two loci YNR008W and YNL313C. See the format of multilocus data here. Note that our method is able to handle missing data, see the example below.optional

    -cl chainLength

    The length of the MCMC chain. The default value is 1,000,000.

    optional

    -bl burnInLengthThe number of iterations in burn-in period. The default value is 200,000.optional

    -sf sampleFrequency

    The sample frequency. The default value is 5,000.

    optional

    -sd seedThe random seed. The default seed is 12345678.optional
    -pl parallelThreads The number of threads running in parallel. The default value is the number of threads in your machine.optional
    -dir outDirectoryThe absolute path to store the output files. The default path is your home directory.optional
    MC3 Settings
    -mc3 temperatureList

    The list of temperatures for the Metropolis-coupled MCMC chains. For example, -mc3 (2.0, 3.0) indicates two hot chains with temperatures 2.0 and 3.0 respectively will be run along with the cold chain with temperature 1.0. By default only the cold chain will be run. Note that

    • The temperatures should be DIFFERENT! For example, -mc3 (2.0, 2.0, 3.0) is invalid.
    • The temperature of the cold chain should NOT be included. For example, -mc3 (1.0, 2.0, 3.0) is incorrect.
    		optional
    Inference Settings
    -mr maxReticulationThe maximum number of reticulation nodes in the sampled phylogenetic networks. The default value is 4.optional

    .0. By default only the cold chain will be run. Note that

    • The temperatures should be DIFFERENT! For example, -mc3 (2.0, 2.0, 3.0) is invalid.
    • The temperature of the cold chain should NOT be included. For example, -mc3 (1.0, 2.0, 3.0) is incorrect.
    • Metropolis-coupled MCMC leads to faster convergence and better mixing, however, the running time increases linearly with the number of chains.
    		optional
    Inference Settings
    -mr maxReticulationThe maximum number of reticulation nodes in the sampled phylogenetic networks. The default value is 4.optional
    -tm taxonMapGene tree / species tree taxa association. By default, it is assumed that only one individual is sampled per species in gene trees. This option allows multiple alleles to be sampled. For example, the gene tree is (((a1,a2),(b1,b2)),c); and the species tree is ((A,B),c);, the command is -tm <A:a1,a2; B:b1,b2;c:c>. Note that the taxa association should cover all species, e.g. -tm <A:a1,a2; B:b1,b2> is incorrect because c:c is dropped out-tm taxonMapGene tree / species tree taxa association. By default, it is assumed that only one individual is sampled per species in gene trees. However, this option allows multiple alleles to be sampled. optional
    -fixps popSizeFix the population sizes associated with all branches of the phylogenetic network to this given value. By default, we estimate a constant population size across all branches.optional
    -varypsVary the population sizes across all branches. By default, we estimate a constant population size across all branches.optional
    Prior Settings
    -pp poissonParamThe Poisson parameter in the prior on the number of reticulation nodes. The default value is 1.0

    optional

    -ddDisable the prior on the diameters of hybridizations. By default this prior on is exp(10).optional
    -eeEnable the Exponential(10) prior on the divergence times of nodes in the phylogenetic network. By default we use Uniform prior.optional
    Starting State Settings
    -sgtSpecify the starting gene trees for each locus. Comma delimited list of gene tree identifiers. See details. The gene trees should be ultrametric trees with coalescent times in units of expected number of mutations per site. See example below. The default starting gene trees are UPGMA trees.optional
    -snetSpecify the starting network. The input network should be ultrametric with divergence times in units of expected number of mutations per site, inheritance probabilities and population sizes in units of population mutation rate (optional). See example below. The default starting network is the MDC trees given starting gene trees. optional
    -spsSpecify the starting population size. The default value is 0.036. See example below.optional
    -preSpecify the number of iterations for pre burn-in, e.g. "-pre 20" means 20x sampleFrequency iterations will be run before the MCMC chain starts. By default, we run 10x sampleFrequency iterations for pre burn-in.optional

    Substitution Model

    -gtr paramListSet GTR (general time-reversible) as the substitution model. The first four parameters in the list represent base frequencies for A, C, G, T. The rest six parameters represent transition probabilities for A>C, A>G, A>T, C>G, C>T and G>T. The default substitution model is JC69 model.optional
    Phasing
    -diploid diploidSpeciesListIntegrates over all possible phasings of heterozygous genotypes when computing likelihoods [2] given diploid species list. For example, a list of (Scer, Spar) indicates species Scer and Spar will be treated as diploid species in likelihood computation. See Section S4 in G-PhoCS manual for full details. By default we assume the sequences come from haploid species, or the sequences are randomly phased. Note that the substitution model is set to JC69 (fixed).optional

    Simple Example

    Code Block
    htmllang
    #NEXUS 
Begin data;
	Dimensions ntax=5 nchar=80;
	Format datatype=dna symbols="ACTG" missing=? gap=-;
	Matrix
[YAL053W, 25, ...]
Scer TCTTTATTGACGTGTATGGACAATT
Spar TCTTTGTTAACGTGCATGGACAATT
Smik TCCTTGCTAACATGCATGGACAATT
Skud TCTTTGCTAACGTGCATGGATAATT
Sbay TCTTTACTAACGTGCATGGATAACT
[YAR007C, 30, ...]
Scer ATGAGCAGTGTTCAACTTTCGAGGGGCGAT
Spar ATGAGCAGCGTTCAACTTTCGAAGGGCGAC
Smik ATGAGCAGCGTGCAACTATCAAAGGGCGAC
Skud ATGAGCAGTGTTCAACTTTCGAAGGGCGAC
Sbay ATGAGCAGCGTTCAACTTTCGAAGGGCGAC
[YBL015W, 25, ...]
Scer TCTAATTTGTTAAAGCAGAGAGTTA
Spar TCTAATTTGTTAAAGCAGAGAGTTA
Smik TCTAATTTGTTAAAACAGAGAGTTC
Skud TCTAATCTGTTGAAGCAGAGAGTTA
Sbay TCTAATCTGTTGAAGCAAAAAGTCA
;End;
BEGIN PHYLONET;  
MCMC_SEQ -cl 250000 -bl 50000 -sf 5000;
END;

     

    ...