Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_61 Phylogentic Analysis by Maximum Likelihood -PAML at MUSC.

This software written by Ziheng Yang of the Galton Laboratory,
University College London. The current MUSC release is 4.02
May 2000.

PAML is a suite of programs

BASEML -nucleotide data analysis
BASEMLG -nucleotide data analysis with continuous gamma
CODEML - codon or amino acid analysis
EVOLVER -simulating sequence datasets
MCMTREE -Bayesian estimation of phylogenies
PAMP -parsimony based analysis
yn00 -estimates synonymous/nonsynonymous substituition rates


Each program is run in conjunction with a control file. For instance

codeml aaml.ctl

Where aaml.ctl is a control file for amino acid sequence

Consult the PAML manual
 for details.

Here's a control file for yn00:
      seqfile = abglobin.nuc * sequence data file name
      outfile = yn           * main result file
      verbose = 0  * 1: detailed output (list sequences), 0: concise output

        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below

    weighting = 0  * weighting pathways between codons (0/1)?
   commonf3x4 = 0  * use one set of codon freqs for all pairs (0/1)? 



* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.

Here's a control file for mcmctree

seqfile = mtprim9.nuc  * sequence data file name
    outfile = mcmctree.out * main result file name
   treefile = 9s.trees     * tree file for initial rooted tree topology

     LHfile = LHs  * LH file name, read (MCMC=0) or rewritten (MCMC=1)
       MCMC = 1     * 0: read LHs from LHfile, 1: use MCMC to generate LHs
       beta = 0.15  * prob{labeled history change}, used only if MCMC=1
       seed = 1234567 * random number seed

     delta0 = .5     * small number for MCMC, used if MCMC=1 only
     delta1 = .5     * smaller number for comparing candidate LHs

      model = 3      * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
      kappa = 1.63 2.127  * kappa in K80, F84, or HKY85
      alpha = 0      * alpha for gamma rates at sites
      ncatG = 4      * No. categories in discrete gamma

   hierarch = 0      * 1:hierarchical; 0:empirical Bayes analysis
      birth = 6.7    * birth rate
      death = 2.5    * death rate
     sample = .06   * sampling fraction
     mutate = .24 * mutation rate (# of mutations from root to present)

Here's a control file for baseml

      seqfile = brown.nuc * sequence data file name
      outfile = mlb       * main result file
     treefile = brown.trees  * tree structure filename

        noisy = 3   * 0,1,2,3: how much rubbish on the screen
      verbose = 0   * 1: detailed output, 0: concise output
      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
                    * 3: StepwiseAddition; (4,5):PerturbationNNI 

        model = 4   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:TN93, 6:REV, 7:UNR
EST
        Mgene = 0   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff

    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
        kappa = 5  * initial or fixed kappa

    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
        alpha = 0.3  * initial or fixed alpha, 0:infinity (constant rate)
       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
        ncatG = 8   * # of categories in the dG, AdG, or nparK models of rates

      fix_rho = 1   * 0: estimate rho; 1: fix rho at value below 
          rho = 0.  * initial or fixed rho,   0:no correlation
        nparK = 0   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK 

        clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:TipDate
        nhomo = 0   * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
        getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 1   * (0,1,2): rates (alpha>0) or ancestral states

*   Small_Diff = 4e-7
*    cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
*        ndata = 1

*        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
        method = 0   * 0: simultaneous; 1: one branch at a time



These are all programs with plain text 
user interfaces ( ie no fancy GUI).

    

The BCR at the Medical University of South Carolina

 URL: http://bcr.musc.edu/

  Last modified:
 June 2, 2000- ESH 



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