New upstream version 4.9i+dfsg

https://groups.google.com/forum/#!forum/pamlsoftware.

Version 4.9i, March 2019

(*) mcmctree: I have added an option (duplication = 1) for dating a

tree with both speciations and gene duplications, so that some nodes

on the tree share divergence times.  Nodes sharing ages are identified

using labels in the tree file: #1, #2, ....  I have yet to update the

document about specification of the model.

(*) mcmctree: The TipDate option was written for one locus or

partition and never worked for more than two loci/partitions.  I have

edited the code so that it works for multiple partitions, some of

which may be molecular and the others morphological.

(*) codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7

(FMutSel) is not working in versions 4.9g and 4.9h.  This is fixed

now.  This option uses the observed codon or amino acid frequencies

for the mutation-selection models of codon usage.  Instead the program

estimates the frequencies using maximum likeihood, which is what the

option estFreq = 1 does.  Look at the README file in the

examples/mtCDNAape/ folder.

(*) codeml clade model D: The bounds for the w (dN/dS) ratios in the

first site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for

w1, in versions 4.9b,c,d,e,f,g, since I added the BEB calculation for

clade model D in 4.9b.  The motivation for the bounds is that site

class 0 represents strong purifying selection with a small w0, while

site class 1 should include sites under weak purifying selection with

a larger w1.  However the bounds are arbitrary.  In some datasets, the

MLEs are found to be at the bounds, making the interpretation awkward.

I have changed the bounds to the following: 

w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}.

This means that the user should swap the estimates of w0 and w2 if w0 > w1.

Version 4.9h, March 2018

(*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for

 7  1

((((human, (chimpanzee, bonobo)) '>.06<.08', gorilla),

(orangutan, sumatran)) '>.12<.16', gibbon);

((((human, (chimpanzee, bonobo)) '>.06<.08', gorilla), (orangutan, sumatran)) '>.12<.16', gibbon);

//end of file

((((human, (chimpanzee, bonobo)) 'B(.06, .08)', gorilla),

(orangutan, sumatran)) 'B(.12, .16)', gibbon);

((((human, (chimpanzee, bonobo)) '>.06<.08', gorilla), (orangutan, sumatran)) '>.12<.16', gibbon);

((((human, (chimpanzee, bonobo)) 'B(.06, .08)', gorilla), (orangutan, sumatran)) 'B(.12, .16)', gibbon);

    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below

        kappa = 2   * initial or fixed kappas

    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below

    fix_alpha = 1   * 0: estimate alpha; 1: fix alpha at value below

        alpha = 0.25   * initial or fixed alpha, 0:infinity (constant rate)

        ncatG = 5   * # of categories in the dG, AdG, or nparK models of rates

      fix_rho = 1   * 0: estimate rho; 1: fix rho at value below