History and bug fixes of PAML (Phylogenetic Analysis by Maximum Likelihood)

Ziheng Yang


If you find problems or have questions, please visit the PAML
discussion site
https://groups.google.com/forum/#!forum/pamlsoftware.



Version 4.9e, March 2017

Edited the readme files to change the license to GPL.



Version 4.9d, February 2017

(*) mcmctree.  A bug was introduced which causes the program to read
the fossil calibration information in the tree file incorrectly, if
lower (minimum) bounds are specified using the symbol '>'.  If you use
the notation "B()" or "L()", the information is read correctly.  This
bug was introduced in version 4.9b and exists also in 4.9c.  Versions
4.9a and earlier were correct.

(*) mcmctree.  Changed the default prior for rates for loci to
gamma-Dirichlet (dos Reis 2014), and updated the documentation as
well.  It was set to the conditional i.i.d. prior (Zhu et al. 2015).

(*) mcmctree.  Added Bayes factor calculation.  A program called
BFdriver is included in the release, as well as a pdf document in the
folder examples/DatingSoftBound/BFdriverDOC.pdf.  We suggest that you 
use the exact likelihood calculation when you use this option, since the 
normal approximation is unreliable when the power posterior is close to 
the prior (when beta is small).




Version 4.9c, September 2016

(*) Added GPL license statement in various places.

(*) codeml.  When two or more trees are in the tree file and the
specified model is the branch model, the program counts the number of
parameters correctly only for the first tree.  For the second or later
trees, it overcounts the parameters in the model.  The lnL and
parameter estimates are still correct, but the printed values for the
extra parameters are more or less random numbers and vary among
different runs of the same analysis.  The bug was introduced in
version 4.7a and affects the versions since then until 4.9b.  It is
now fixed.  Thanks to Casey Bergman.



Version 4.9b, March 2016

(*) codeml.  I have added the BEB calculation for clade model D.  I
deleted the option of having two site classes under model D so that
both clade models C and D now assume three site classes.  The
difference between models C and D is that in C, w1 = 1 is fixed, while
in D, w1 is a free parameter, just like w0.  Both the ML iteration and
the BEB calculation under models C and D allow two or more clades
(branch types), but note that an increase in the number of clades by 1
roughly increases the computation by 10 times.  Also the BEB
calculation under model D is about 10 times more expensive than that
under model C.  I updated the codeml section of the documentation to
remove the description of the old models (like M1 and M2) and focus on
the new models that are in the program (like M1a and M2a).

baseml & codeml.  If the tree has labels using the symbol #,
the program will crash.  This is caused by a bug in the routine for
reading trees from the tree file.  This is now fixed.



Version 4.9a, September 2015

codeml (seqtype = 2 for amino acid sequences) crashes when the dataset
is large, with more than 2M sites, say.  This is due to a stupid bug
in an irrelevant part of the code.  This is fixed in 4.9a.


Version 4.9, January 2015

(*) mcmctree.  There are now two priors for locus rates (mu_i or rates
for loci), as summarized in Zhu et al. (2014 Sys Biol).  They are
specified as follows

   rgene_gamma = alpha_u beta_u alpha prior  * gamma prior for overall rates for genes

where prior = 0 (default) is the conditional i.i.d. prior and prior =
1 is the gamma-dirichlet prior.

For example the following specifies the conditional i.i.d. prior with
alpha_mu = 100, beta_mu = 1000, and alpha = 0.5.  Here the average
overall rate is 0100/1000 = .1 changes per site per time unit.  alpha
= 0.5 describes the extent of rate variation among loci.

   rgene_gamma = 100 1000 0.5 0  * conditional i.i.d. prior for locus rates
  sigma2_gamma = 4 100 0.5       * prior for sigma^2     (for clock=2 or 3)

The sigma2_i prior has parameters alpha_u, beta_u, alpha, specified in
the same format.  

(*) mcmctree.  I have changed the option of setting the finetune step
lengths for the MCMC algorithms so that each parameter in the model
has its own step lengths.  As a result, the step lengths are all
automatically adjusted during the burn-in, and cannot be fixed or
specified by the user.  The line 
  finetune = 1: .0040  0.030  0.015  0.03 .55  * times, rates, mixing, paras, RateParas
in the control file, if present, is read but ignored.  

(*) mcmctree.  The calibration density for S2N (skew 2 normals) is
incorrectly implemented.  While the correct formula should be 
  p0 * f1(t) + (1 - p0) f2(t)
the incorrect formula used is 
  p0 * f1(t) + f2(t).
Basically the two skew-normal densities was not given the correct weights.
If you run the program without data to make sure that the effective prior 
is sensible, then this mistake should have little impact.  The bug is now 
fixed.  Thanks to Mario dos Reis.




Version 4.8a, August 2014

(*) baseml (nhomo = 3 or 4).  I have added the nonhomogeneous GTR
(REV) model with a set of abcde parameters for every branch.  The
specifications are as follows.

model=7 nhomo=4 fix_kappa=0: one set of rate parameters abcde in GTR for the whole tree.
model=7 nhomo=4 fix_kappa=1: one set of rate parameters abcde in GTR for every branch.

In version 4.8, only the second option (one set of abcde parameters
for the whole tree) is implemented, no matter whether you choose 0 or
1 for fix_kappa.  After this change, the use of fix_kappa in the nhomo
models is consistent between HKY and GTR.  For HKY, the specifications
have always been as follows.

model=4 nhomo=4 fix_kappa=0: one kappa in HKY for the whole tree.
model=4 nhomo=4 fix_kappa=1: one kappa in HKY for every branch.
 
Note that nhomo=4 means one set of frequency parameters for every
branch on the tree.

I have also added a method for calculating the expected number of
changes from any nucleotide i to nucleotide j along every branch under
the nonhomogeneous models (nhomo=3 or 4).  This is called EMC, and
accounts for the fact that the base frequencies are changing over
time, and so does the rate of substitution.  It is invoked by using
RateAncestor = 1 and verbose = 1.

I tested only the nhomo=4 option carefully and the options nhomo=3 and
5 are not well tested.



Version 4.8, March 2014

(*) mcmctree.  The prior for rates for loci (with ndata = 2 or more)
has changed in this version, and the gamma-Dirichlet prior is used.
The old i.i.d. prior is replaced and unavailable anymore.  The new
gamma-Dirichlet prior is decribed in a paper 

dos Reis, M., T. Zhu, and Z. Yang. 2014. The impact of the rate prior
on Bayesian estimation of divergence times with multiple
loci. Syst. Biol. 63:555-565.

(*) codeml.  Added a Bayesian method for estimating distance t and dN/dS
ratio w in pairwise comparisons.  The option is 
      runmode = -3  * -3: pairwise Bayesian
      runmode = -3 1.1 1.1 1.1 2.2   * -3: pairwise Bayesian
The four numbers are the parameters in the gamma priors for t and w (a_t b_t a_w b_w).
The method is described in the following paper:

Angelis, K., M. dos Reis, and Z. Yang. 2014. Bayesian estimation of
nonsynonymous/synonymous rate ratios for pairwise sequence
comparisons. Mol. Biol. Evol. 31:1902-1913.

(*) baseml, codeml, mcmctree).  In version 4.7a, I disabled the option
of reading species indexes in the tree file (for example, the number
19, instead of the sequence name, may be used in the tree file to mean
the 19th sequence in the sequence alignment).  I have added this back.
Version 4.7 does not have this problem.

(*) codeml in paml 4.6 and 4.7 has a bug if your sequences have stop
codons.  Stop codons have always been disallowed in the codon models
implemented in codeml.  In versions 4.6-4.7, if there is a stop codon
in any sequence, the codons in all sequences at that site (column in
alignment) are changed into ??? and then the sequences are processed
in the usual way.  The likelihood should then be the same as the
likelihood if that column is removed from the alignment.  However, the
implementation of the idea was incorrect and gives wrong results if
the sequences do not contain any ambiguity characters and if you
choose cleandata = 0.  I have now fixed this.  The idea is not really
useful, so the good advice is that you delete the column of stop
codons before the data are analyzed using codeml.
 

Version 4.7a, October 2013

(*) codeml.  The mutation-selection model of Yang and Nielsen (2008)
is noted to work for the site and branch-site models but not for the
branch models.  This is now fixed.

(*) mcmctree.  I fixed and modified the infinitesites program, which
generates the limiting distribution when the amount of sequence data
approaches infinity.  This works for both the clock (clock=1) and
relaxed clock models (clock=2 or 3).  The mcmctree tutorial explains
how to run this program.


Version 4.7, January 2013

(*) mcmctree.  This version includes a method for dating divergences
using sampled tips, as in viral datasets.  The prior for node ages in
the given rooted tree is generated using a
birth-death-sequential-sampling model, described in Stadler and Yang
(2012 Syst Biol, submitted).  The SIV/HIV-2 example dataset analyzed
in the paper is in the examples/TipDate/ folder.  Look at the readme
file there.

(*) codeml.  Version 4.6 crashes if you have a lot of ambiguity codons
in the alignment, or precisely if the total number of fully determined
codons (61 in the standard code) and the ambiguous codons exceed 127.
I was using "unsigned char" to represent the codons, which go from 0
to 255 and can represent 256 distinct codons.  Somehow I changed this
to "char", which on some systems goes from -128 to 127.  Can't
remember why I made the change.  Anyway this is now fixed.  Versions
4.5 or earlier do not have this problem.  Thanks to David Yu for
pointing out the problem.



Version 4.6, September 2012

(*) baseml. The model of autocorrelated-rates among sites (Yang 1995
Genetics 139:993-1005) is broken in paml versions 4.3 to 4.5
inclusive.  Earlier versions were apparently fine.  When you select
the auto-discrete-gamma model (alpha > 0, rho > 0) or the
nonparametric autocorrelated-rates model (fix_alpha = 0, ncatG = 3,
nparK = 4), the program aborts with the following error message:

"Error: use 10, 20, 32, 64, 128, 512, 1024 for npoints for legendre.."

This is now fixed.  The option of nparK = 3 seems to have problems in
all versions, and the program prints out the following warning
message.  

"nparK==3, double stochastic, may not work.  Use nparK=4?"

This option is supposed to fit a Markov-dependent model with equal
proportions in the rate categies.  I have not got time to investigate
this option, but a glance at table 3 in that paper indicates that this
model was not used in the table and probably never properly
implemented, so please follow the advice and use nparK = 4 instead.

(*) codeml.  I have now added the site model M2a_rel of Weadick & Chang
(2012 Mol. Biol. Evol.), in which w2 > 0.  This is specified using
NSsites = 22 while model M2a is specified as NSsites = 2 (with w2 >
1).  M2a_rel is the null model for the likelihood ratio test based on
clade model C, suggested by Weadick & Chang (2012 Mol. Biol. Evol.).
Note that the very old site model M2 from Nielsen & Yang (1998
Genetics) assumes w0 = 0.  Yang, Wong, Nielsen (2005 MBE) changed the
model so that 0 < w0 < 1 and renamed the model M2a.  My tests using
the versions around that time reveals the following:

3.13d (M2):  w0 = 0, w2 > 0
3.14a (M2a): w0 > 0, w2 >= 1
3.14b (M2a): w0 > 0, w2 >= 1

If seems that when we changed M2 into M2a, we also changed the
constraint on w2.  I don't have a copy of version 3.14 to check.

(*) basseml & codeml.  To following option
    bootstrap = 1000

should produce 1000 bootstrap samples in the file boot.txt.  A bug is
introduced in versions 4.4 and 4.5, so that garbiage is created
instead of bootstrap datasets.  Versions 4.3 and earlier were correct.
This bug is now fixed.

(*) evolver.  The simulation of codon sequences (evolver 6
MCcodon.dat) is incorrect when a genetic code different from the
universal code is used.  This is a conceptual error I made and it has
been in all previous versions when simulation of codon sequences is
allowed.  I have assumed incorrectly that setting the frequencies of
stop codons to 0 should be sufficient to get correct results.  The
zero frequencies allow the program to identify the stop codons
correctly, but one still needs the code table to know which changes
are synonymous and which nonsynonymous.  evolver has been using the
universal code to simulate codon sequences.  Simulation using the
universal code has been correct, and simulation using the
mitochondrial code (for example) is affcted and the results should be
incorrect although the impact may be slight.  This bug is now fixed.
A variable is added in the control file MCcodon.dat right below the
codon frequencies, which tells the program which genetic code to use.

1   * genetic code (0:universal; 1:mammalian mt; 2-10:see below)

The program also checks that the stop codons have frequency 0 and that
the frequencies of the sense codons sum to 1.  Thanks to Mario dos
Reis for pointing this out.

(*) mcmctree.  A bug is found in the calculation of the prior on rates
under the correlated-rates model (clock=3).  This bug has been in
version 4 (July 2007) to version 4.5 (December 2011), inclusive.  The
prior is calculated by multiplying the conditional densities of
equation (7) in Rannala & Yand (2007) over all interior nodes on the
master tree (see also Figure 1 in that paper).  However, the rA used
in the program was not for the current branch: it was instead for the
ancestral branch.  The correct formula used was correct for the root
of the master tree, but incorrect for other interior nodes.  The
impact of the bug on posterior time estimates may be expected to be
small, but if the clock is seriously violated and rates change over
neighboring branches, this may be a concern.



Version 4.5, December 2011

baseml.  I have added the joint ancestral reconstruction under the
nonhomogeneous models (nhomo = 3 or 4).  This works for the model of
one rate for all sites, and does not work for the model of gamma rates
for sites or the partition models.  Also I implemented the joint
reconstruction only and not the marginal reconstruction.

mcmctree.  The program now prints out a file called FigTree.tre in the
current working directory that is readable by FigTree.  The branch
lengths show the posterior means of times while the bars generated by
FigTree will indicate the 95% CIs.  I have also added an option to
deal with TipDate data, such as viral sequences with dates.  See
examples/TipDate/README.txt for more notes.



Version 4.4e, May 2011

mcmctree.  I have added an option of automatically adjusting the step
lengths for proposals in the MCMC algorithm.  The program will use the
burn in to automatically adjust the step lengths, using those values
specified in the control file as initial values.

codeml: The iteration method that updates one branch length at a time
(method = 1) is broken for the free-ratios model (model = 1) from
versions 4.3 to 4.4d inclusive.  When codeml runs, you will see
messages like the following on the screen: 
Warning rounding error? b=3 cycle=0 lnL=6036.9413757 != 6070.1069284 
Version 4.2 and earlier are correct.  This bug is now fixed.  
Thanks to Tae-Kun Seo for reporting the bug.



Version 4.4d, March 2011

yn00.  The option of using weighting (weighting = 1) in the
calculation of dN and dS by the YN00 method (Yang and Nielsen 2000)
has been broken since Version 4.4 (February 2010).  A bug was
introduced when I changed the character coding in Version 4.4, so that
this bug affects Versions 4.4, 4.4a, 4.4b, and 4.4c.  The bug
typically causes a crash.  The result for weighting = 0 is not
affected.  Versions before 4.4 are correct.  This bug is now fixed.
Thanks for Charlie
(http://www.ucl.ac.uk/discussions/viewtopic.php?t=8726&highlight=yn00).



Version 4.4c, August 2010

mcmctree.  A bug causes the exotic calibrations (gamma, skew normal
and skew t) to be sometimes ignored, if you have multiple loci
(partitions) and if some species/sequences are missing at some loci.
If all calibrations are bounds (minimum, maximum, and joint), or if
the partitions have the same number of species/sequences, the
calculation is still correct.  This bug is in versions 4.1-4.4b.  This
is now fixed.  Thanks to Mike Steiper.



Version 4.4b, July 2010

mcmctree.  A serious bug has been discovered which affects the option
of approximate likelihood calculation (usedata = 2).  If the first
child of the root in the tree for any locus is a tip, the MLEs of
branch lengths in the in.BV file are assigned to wrong branches, so
that the results are entirely incorrect, and also very different from
those obtained using the exact likelihood calculation (usedata = 1).
Suppose the tree for a locus is (A, B), with a bifurcation at the
root, and with A and B representing species or clades.  If A is a tip,
the program is incorrect, while if A is an internal node, the program
is correct.  This bug is in versions 4.2b - 4.4a.  Hopefully this is
now corrected.  Thanks to Mario dos Reis.

mcmctree.  I also changed the specification on L, U, and B bounds to
allow the user to specify the tail probabilities (which used to be
fixed at 2.5%) for each fossil calibration.  See table 8 in
pamlDOC.pdf for details.  You will still have to run the program
without data to get the effective prior of times used by the program.



Version 4.4a, June 2010

codeml (RateAncestor=1).  For ancestral reconstruction under codon
models, the program prints out the translated amino acids when it
prints the codons.  A bug caused the translation to be incorrect,
so instead of the amino acid, the program prints something like h or
H.  This bug was introduced in Version 4.4, February 2010 when I
changed the way that the characters are coded.  This is fixed now.

baseml (clock = 1, 2, or 3 Mgene option).  If you assign different
rates for different genes (or site parations) and the model assumes
global clock or local clock, the program fails to print out the
relative rates for genes.  This bug seems to be introduced between
3.13 and 3.14 and has since.  The log likelihood value and estimates
of parameters are all correct, and the problem is only that MLEs of
rates for genes are not printed in the output file properly.



Version 4.4a, April 2010

In versions 4.2, 4.3, 4.4, Clade model D does not print the w
estimates for the site classes correctly.  For the example run in
examples/datasets2/, the incorrect output looks like the following

site class             0         1         2
proportion        0.48590   0.10718   0.40692
branch type 0:    0.10557   4.17186   4.17186
branch type 1:    0.10557   4.17186   3.05340

while the correct results (from version 4.1) are 

site class         0         1         2
proportion       0.48590  0.10718  0.40692
background w     0.10557  4.17186  3.05340
foreground w     0.10557  4.17186  0.95081

The ratios w2 and w3 for site class 2 are incorrectly printed, with w2
equal to w1.  The branch lengths and lnL values etc. are all correct.
This bug affects versions 4.2, 4.3, and 4.4, and version 4.1 and
earlier versions appear to be correct.  Also the bug affects clade
model D, and clade model C appears to be fine.  This is fixed now.
Thanks to cajawe for reporting the bug (see
http://www.ucl.ac.uk/discussions/viewtopic.php?p=28240#28240).



Version 4.4, February 2010

I changed the way that the characters are coded in the programs, which
means that essentially every program in the package is modified.  It
is likely that some bugs are introduced during the process.  

codeml.  The iteration algorithm specified by method = 1 when applied
to amino acid model of gamma rates among sites (seqtype = 2, alpha >
0, method = 1) is broken in versions 4.2-4.3b.  The bug causes the
iteration to fail to converge, with messages like the following
printed on the monitor: 
"Warning rounding error? b=5 cycle=0 lnL=1718.5667685 != 1749.4724545".

mcmctree.  If the gamma prior for rates has alpha <1/3, the initial
values are generated incorrectly.  This is now fixed.



Version 4.3b, November 2009

mcmctree.  A bug was introduced in version 4.2, which causes the
program to ignore the minimum age constraint on the root age and uses
the maximum bound specified by RootAge in the control file, if there
is a calibration on the root and it is a minimum-age constraint.  If
you have no calibration on the root, or if the calibration is an
maximum bound, both minimum and maximum bound or gamma distribution,
there is no problem.  The error affects versions 4.2 and 4.3, and
version 4.1 is correct.  This is now fixed.  Thanks to Mathieu
Groussin.

evolver.  I have now added back the option of printing out the site
pattern counts instead of the sequences (specified at the beginning of
the control file such as MCbase.dat).  Use of pattern counts takes
less disk space.  The option was removed in version 4.2b after the
algorithm for collaspsing sites into patterns was rewritten.



Version 4.3a, October 2009

mcmctree.  A bug was introduced in version 4.3, which causes the root
age to be proposed incorrectly.  The effect of the bug appears to be
subtle and is hard to assess.  It means that the results from all
three clock models (clock = 0, 1, 2) are incorrect.  Here is a bit more
detail about the bug.  The internal maximum node age was set too high,
and caused loss of significant digits in a smart reflection algorithm
which reflects proposed values into the feasible interval.  This
update fixes the bug.  Please use this version to reanalyze your data
if you have used version 4.3.  Version 4.2 does not have this bug.

mcmctree.  I now supplies compiling options so that you can use hard
minimum hard maximum, or hard minimum soft maximum.  The executables
are called mcmctreeHH and mcmctreeHS.  See the commands for compiling
at the beginning of the file mcmctree.c.



Version 4.3, August 2009

mcmctree.  The approximate likelihood calculation was unreliable,
because the Hessian matrix was not calculated reliably, especially if
the maximum likelihood estimates of some branch lengths are 0.  I have
now implemented the approach of Seo, Kishino and Thorne (2004), which
appears to be more stable.

baseml & codeml: I changed these two programs to read fasta alignments
directly, working out the number of sequences and the sequence length
automatically.  However, this does not work when you have multiple
alignments in one file, that is, if ndata = 2 or higher.



Version 4.2b, April 2009

mcmctree. There is a bug that leads to crash when usedata = 3 and when
the data at some loci have ambiguity characters while other loci do
not.  usedata = 3 means that the program invokes baseml or codeml to
calculate the maximum likelihood estimates (MLEs) of branch lengths
and the variances of those MLEs.  The temporary sequence alignment
files for the loci (tmp?.txt) generated by mcmctree have garbiage and
are unreadable by baseml (or codeml).  This bug is now corrected.
(You can replace the wrong alignment file for the locus by your
original alignment and run baseml outside mcmctree.)


All programs.  I rewrote the code for collapsing sites into patterns.
This should have no impact on user files, except that evolver does not
produce data files in the "pattern-count" format anymore.  Now two
formats (paml/phylip format and PAUP nexus format) are used, specified
by the first line of the control data file (e.g., MCbase.dat,
MCcodon.dat, MCaa.dat).  This pattern-count format is still accepted
as input by baseml, codeml, etc. (See the section on "Site pattern
counts" in the documentation).

baseml & codeml.  A bug was introduced to the local clock model
(clock=6), so that the program generates the following error message:
"need fossils for this locus".  For example, running codeml on the
control file /examples/MouseLemurs/codonml2.ctl will do so.  This bug
is now fixed.

codeml: The bug introduced in version 4.2 concerning the free-ratios
model (Yang 1998 MBE) was not fixed properly in version 4.2a (see the
notes for 4.2a below).  The results are incorrect when there are
exactly 7 branch types (for example when you run the free-ratios model
on a 5-species tree) but are correct for other numbers of branch
types.  I hope this is now finally fixed.



Version 4.2a, February 2009


codeml: Two bugs were known to have been introduced in version 4.2
when I rewrote the code for the branch-site and clade models.  The
first is the null hypothesis in the branch-site test (model = 2
NSsites = 2, fix_omega = 1 omega = 1).  The reference for this model
is Yang, Wong & Nielsen (2005), and Zhang et al. (2005).  The
alternative model (fix_omega = 0) is fine.

The second bug is in the free-ratios model (Yang 1998 MBE).

The results from those two models are incorrect and should be ignored
if you used version 4.2.  Both mistakes are fixed in this update.

Thanks to W.P. Zhou and BYLee.



Version 4.2, December 2008

MCMCtree: The implementation of the lower bound and of the upper bound
is changed.  The improper density of equation (15) of Yang and Rannala
(2006) for the lower bound is noted to push up divergence times, a
feature we consider undesirable.  Now a truncated Cauchy distribution
is used instead.  This will be described in more detail somewhere.

The default file name for the MCMC samples is mcmc.out.  To change
this, add the following line in the control file mcmctree.ctl:
      mcmcfile = mcmc.out 

codeml: Clade models C and D are extended to accommodate more than two
branch types.  The old models accept two branch types only, referred
to as foreground and background branches.  The structure of the new
models are below.  You use branch/node numbers to specify the branch
types (with #0 to be the default, followed by #1, #2, #3, ...).  As
before, the BEB calculation is implemented for clade model C only, and
is not available for clade model D.  The BEB calculation is expensive,
so I expect clade model C will work if you have only a few branch
types.  For each additional branch type, the BEB computation is 10
times more expensive.

Site class   Proportion    w ratio

  0             p0         0 < w0 < 1
  1             p1         w1 (w1 = 1 is fixed in model C)
  2             p2         w2, w3, w4, ...

I also added an option of fixing the last w to 1 in clade model C,
specified in the control file as follows.  For example, if there are
three branch types in the tree (see the table above), the last w fixed
will be w4.

       fix_omega = 1
       omega = 1

The two versions of the clade model can be compared to test whether
the last w is > 1.


codeml: branch model with amino acid chemical properties, specified
using model = 2 and aaDist = 7.  Under this model, the types of
branches are specified just like the branch model (by labelling
branches).  For each branch type, the program estimates a few w's,
depending on specifications in the file OmegaAA.dat.  This model seems
to be broken for a long time since its implementation.  Look at the
readme.txt file in examples/mtCDNAape/.



Version 4.1, August 2008

MCMCtree: A few changes have been introduced to this program.  The
format for specifying fossil calibrations in the tree file has been
changed, so that the gamma distribution is specified as 'G(alpha,
beta)' and the old format '>0.6=0.7<0.8' does not work anymore.  The
bounds can be specified using either the old form '<0.8' or the new
form 'U(0.8)'.  Two exotic distributions, skew normal and skew t, are
added, using the format 'SN(location, scale, shape)' and 'ST(location,
scale, shape, df)'.  I edited the documentation pamlDOC.pdf and
rewrote the part for mcmctree.  The format of the MCMC output file
mcmc.out has been modified so that it is readable by Andrew Rambaut's
Tracer program.  Note that MCMCtree starts taking samples and writing
into the file only after burnin.

codeml. The mutation-selection models of Yang and Nielsen (2008
Mol. Biol. Evol. 25, 568-579) are specified using the options

    CodonFreq = 6 or 7  * 6:FMutSel0, 7:FMutSel
      estFreq = 1

Use examples/mtCDNAape/codeml.HC.ctl to duplicate results in table 1
in the paper.  It seems that some results are in the mlc file while
some other results are in the rst and rst1 files.


codeml (branch model): When codon sequences are analyzed under the
branch model (model = 1 or 2, NSsites = 0), the main output file
includes a tree under the line "w ratios as labels for TreeView:".
This line was introduced in version 3.15.  However, the branch lengths
in the tree had the dN values, while I intended them to be the
original branch lengths (which are t, the number of nucleotide
substitutions per codon).  This bug may also affect the results of
ancestral reconstruction under the same branch model.  This bug is
fixed now.


baseml and codeml (discrete-gamma model): My intention has been to use
the mean and not the median to represent all rates in each category
when the discrete-gamma model is implemented.  See Yang (1994
J. Mol. Evol. 39:306-314) for the distinction.  However, a bug caused
a few recent versions to use the median instead.  This affects baseml
versions 3.14c and 3.15, while version 3.14b or earlier and version 4
or later are correct.  codeml in version 4a & 4b were incorrect while
other versions are correct.  I hope both baseml and codeml are correct
from version 4c.


baseml and codeml (branch and clade labels): The local clock models
(clock = 2) in the two programs and also the branch or branch-site
models in codeml use labels to identify branches.  When nested clade
label ($) are used, the program may get confused so that the branches
are not labeled correctly.  I think this is not fixed in version 4c.


Version 4b, January 2008

mcmctree.  Changed a variable name in the control file from MaxRootAge
to RootAge.  This should be specified in any of the following formats: 

       RootAge = <1.0  * constraint on root age, used if no fossil for root.
       RootAge = '<1.0'  * constraint on root age, used if no fossil for root.
       RootAge = <1.0>0.8  * constraint on root age, used if no fossil for root.
       RootAge = '<1.0>0.8'  * constraint on root age, used if no fossil for root.

Added some text around the output, to make the results more comprehensible.

evolver (option 8).  option 8 for calculating bipartition distances
between trees is broken.  I changed the program to prepare for a
figure and forgot to remove the changes afterwards.  This is now
fixed.


Version 4, July 2007

mcmctree.  The MCMC algorithm of Rannala and Yang (2007) dealing with
rate drift is added.  The section of manual on mcmctree is now
rewritten.  An example data set is included in the
examples/DatingSoftBound/ folder.

codeml. This now implements the mutation-selection models of codon
substitution of Yang and Nielsen (2008).  I should include more
details after the models are better tested, for example, after the
paper is written.

baseml.  The log likelihood under the gamma-rates model (that is, when
alpha > 0 in the control file) is not calculated correctly, or not as
intended.  Version 3.14a is correct, but versions 3.14c and 3.15 are
incorrect.  I am not sure about version 3.14b, as I have not kept a
copy.  The bug causes the median to be used to represent all rates in
each category of the discre-gamma model whereas the mean was intended.
See the discussion around equation (10) and the paragraph below it in
Yang (1994. J. Mol. Evol. 39:306-314).  The bug is not expected to
have much effect on tree topologies or branch lengths.  Thanks to
Simon Whelan for reporting the bug.



Version 3.15, March 2006

evolverNSbranches (simulation program to generate data under the
branch models of codon substitution).  A bug was introduced after
version 3.14a so that versions 3.14b (?), 3.14c, and 3.15 have a bug
that makes the program abort prematurely.  This is now corrected.
Thanks to N. Clark for reporting the bug.


Version 3.15, January 2006

evolver.  The simulation option of the evolver program in version
3.14b (?), 3.14c, and 3.15 has a serious bug that makes the program
generate nonsensible sequences when the user tree has 0 internal
branch lengths.  The bug was introduced between versions 3.14a (which
is correct) and 3.14c (which is wrong).  I don't seem to have kept
3.14b to check whether it is in error.  In this case, the smart idea
that led to the bug was the thought that no evolution occurs if the
branch length is 0 (or less than 1e-20, to be more precise).  If the
branch length is 0, there is no need to evolve the sequence along the
branch, so I decided to copy the sequence at the start of the branch
to the node at the end of the branch.  This would be fine, except that
I introduced a bug at the same time that caused the program to skip
generating sequences at all nodes that are descendents of the
zero-length branch.  As a result, sequences at tips that are
descendents of the zero-length branch have no data.  On some systems
the uninitialized space is initialized as 0, and then the sequences
will be printed out as consisting of all Ts (T is the first nucleotide
in my program).


At the same time, I also turned on the option of simulating data on
random trees in evolver.  You change fixtree=1 into 0, and recompile.
Then use MCbaseRandomTree.dat to simulate data instead of MCbase.dat:

    evolver 5 MCbaseRandomTree.dat



Version 3.15,  November 2005

mcmctree: This implements the MCMC algorithm of Yang and Rannala (2005
MBE) for estimating species divergence times using soft bounds.  The
example file is in examples/SoftBound/.  Look at the readme file and
see whether you can duplicate our results in the paper.  Note that
this program works with DNA sequence data only, and assumes the
molecular clock (clock = 1).  Note that assumption of the clock can
lead to seriously biased results if the clock is violated.  Work is
under way to relax the clock assumption.  

yn00: Added three methods for estimating dS and dN: LWL85 (Li, Wu &
Luo 1985), LPB93 (Li 1993; Pamilo and Bianchi 1993), and LWL85m (Yang
2006 Computaional Molecular Evolution, Oxford University Press.  Eqs.
2.12 & 2.13).

codonml.  Added example files for clade model C, in folder
examples/CladeModelC.  Thanks for Joe Bielawski for preparing these.

Added a sequence data format, in which the numbers or frequencies of
site patterns are inputed instead of the sequences.  The format is
indicated by the option variable P on the first line of the data file,
used in the same way as option variables I (for interleaved format)
and S (for sequential format, which is the default).  See the section
on sequence data format in the paml documentation for details.  The
old control variable readpattf for baseml and codeml is now deleted.
You can also use evolver to simulate data using this format.  Look at
the control files MCbase.dat, MCcodon.dat, and MCaa.dat.  This format
is useful for very large data sets with >1M sites, when collapsing
sites into patterns can take a long time.  



Version 3.14b, May 2005

pamp crashes when there are more than 127 or 255 (depending on the
system) species in the data.  The bug is due to my declaration of the
variable visit[] in the routine PathwayMP1 in pamp.c as char rather
than int.  Another problem is that the formula used to calculate
distances under REV (GTR) is sometimes inapplicable and the program
prints out messages like "err: DistanceREV".  I introduced some ad hoc
way of dealing with the problem.



Version 3.14b, April 2005

aaml (codeml with seqtype = 2): 

Under the REV model (model = 9), codeml failed to print out the
estimated amino acid substitution rate matrix.  This is fixed.


aaml (codeml with seqtype = 2 or 3):

If you have multiple data sets (ndata > 1) and analysing protein data
sets under the empirical models such as wag, jtt, dayhoff.  The
results for the first data set are correct, but all later data sets
are analyzed incorrectly under the corresponding +F models, that is,
wag+F, jtt+F, dayhoff+F.  A bug in the program means that for the
second and later data sets, the equilibrium amino acid frequencies are
from the real data and not correctly set to those specified by the
empirical models.  Thanks to Ben Evans.


Version 3.14b, February 2005

codonml and aaml:

There is a bug that affects the joint reconstruction of ancestral
sequences when some branch lengths are equal to each other and when
those branches are visited one after the other in the program.  For
example, if some branch lengths are estimated to be 0, such a problem
might occur.  I think this bug is in the program for a long time,
although I note that joint ancestral reconstruction is turned off in
some versions for other reasons.  The marginal reconstruction is not
affected by this bug.  The update fixes this bug.


baseml and codeml:

The program crashes on some systems for the local clock models (clock
= 5 and 6) after the calculation is finished.  If you manage to run
the model, the results should be fine.  There are bugs in the program
when freeing memory at the end of the calculation.  They are fixed in
this update.  See the discussion site at

http://www.rannala.org/phpBB2/viewtopic.php?t=228

Thanks to fjvera.



Version 3.14a, December 2004

codonml (codeml for codons):

The mechanisctic amino acid substitution models (table 3 in Yang et
al. 1998 MBBE 15: 1600-1611) appear to be broken in paml/codeml
versions 3.13 and 3.14.  They were correct in version 3.12.  This is
now fixed.  If you use those models, please run the examples in the
folder examples/mtCDNA/ and compare results with those published in
the paper to confirm the program.  The results in the paper are
correct, but the program implementation may be broken due to lack of
maintenance.

codonml (codeml for codons)

When you fit the branch models with three or more branch types (omega
ratios), the program aborts with an error message saying that only two
omega ratios are allowed.  This is due to a bug in the program and is
now fixed.


Version 3.14, September 2004


1. codonml (codeml for codons): 

(1a) NSsites models M1 (neutral), M2 (selection), and M8 (beta& ) have
been changed.  The references are two manuscripts that are not yet
published (Wong, Yang, Goldman & Nielsen, 2004 Genetics 168:
1041-1051; Yang, Wong, and Nielsen 2005 MBE).  The details are as in the
following table.

[table missing or never written.]

The old models M1 and M2 are noted to be rather unrealistic as they do
not account for sites with 0 < w0 < 1.  Thus in the new models 0 < w0 < 1
is estimated from the data.  Also insisting on a class of sites with 0
= 1 appears to help avoid false positives as sites under weak
selection will be absorbed in this neutral class rather than being
claimed to be under positive selection.  Under M8, the constraint s >
1 is now automatically enforced to help avoid multiple local peaks and
also to make the model a positive-selection model.  Note that the
newer models replace the old ones, which are available in older
versions of paml/codeml only.

After the changes, the models are nested as follows: M0 (one ratio) <
M1a (NearlyNeutral) < M2a (PositiveSelection) < M3 (discrete), and M7
(beta) < M8 (beta& ), where "<" means the model on the left is a
special case of the model on the right:.  Two LRTs can be constructed
using those models.  The first one compares M1a against M2a, using a
chi square with df 2, and the second one compares M7 against M8, using
a chi square with d.f. = 2.

(1b) Similarly branch-site model A (Yang and Nielsen 2002) is changed.
The old model assumes 0 = 0 and is unrealistic.  This is replaced by 0
< 0 < 1, estimated from the data.  The new model is still called
branch-site model A.  It can be compared with the new M1a
(NearlyNeutral) to form a likelihood ratio test, with d.f.  2.  This
is called test 1.  Another test, called test 2, uses a null model A
but with 2 = 1 fixed (use fix_omega = 1 and omega = 1).  Test 2 is
very conservative, but test 1 might mistake relaxed selective
constraint on the foreground branch as positive selection.


(1c) Similarly the clade model C ( see also Forsberg and Christiansen
2003; Bielawski and Yang 2004) is changed as follows.  The new model C
replaces 0 = 0 by 0 < 0 < 1 and has five parameters in the
distribution: p0, p1, 0, 2, and 3.  The new model C can be compared
with the new M1a (NearlyNeutral), with d.f.  3.

(1d) The empirical Bayes procedure for calculating posterior
probabilities of site classes under the site models, branch-site
models, and clade models are called naïve empirical Bayes (NEB).  They
are naïve because they use the MLEs of parameters without accounting
for sampling errors in them.  This problem is now fixed using a
procedure called Bayes empirical Bayes (BEB) (Yang, Wong, and Nielsen
2005).  The BEB procedure is implemented for the site models M2a and
M8, the (modified) branch-site model A, and the (modified) clade model
C.  The old NEB calculation is kept in the output and the new BEB
results follow the NEB result.  Perhaps I will remove the NEB
calculation in later versions.


baseml/codeml: rewrote likelihood clock and local clock models.
Implemented models for combined analysis of multiple genes
incorporating multiple calibration points (Yang and Yoder 2003).  The
ad hoc rate smoothing procedure of Yang (2004) is implemented for
nucleotide, amino acid, and codon substitution models, and the
implementation also deals with missing species at some loci.  The
option variable clock in the control files is now used differently
from before.  See later in this documentation and also the readme and
readme2 files in the folder examples/MouseLemurs/.

baseml/codeml local clock models.  clock = 5 and 6 are added in
3.14beta5.

codeml: added branch-site models C and D (Bielawski and Yang in press).

mcmctree: this program is disabled in this release.  The old program
died and the new program is still under construction.

The main body of this documentation may not be up to date. 



Bug fixes and minor corrections


baseml/codeml.  The output in the file rates under the gamma model
lists inferred rate for each site.  The output is incorrect if the
tree is large and scaling is used to avoid underflow.  The use of
scaling is indicated by two lines of output on the monitor like the
following:

"2 node(s) used for scaling (Yang 2000 J Mol Evol 51:423-432):
 155 350".  

The results are clearly wrong as the probabilities are much greater
than 1, and the rates are many orders of magnitude too large, etc.
Also under the same problematic condition the expected numbers of
sites with certain site patterns in the file lnf are incorrect.  When
scaling is not used, the results should be o.k. and look reasonable.
This affects versions 3.13 and 3.14beta1-3.  This is fixed in version
3.14.  Thanks for Nick Goldman for pointing out the error.

yn00.  The program crashes for large datasets with many codons due to
a memory allocation error.  This affects versions 3.13 and some
versions of 3.14beta1.  The problem is fixed in version 3.14.

aaml (codeml for amino acids).  Model REVaa_0 is broken due to lack of
maintenance in versions 3.1, 3.11, 3,12, 3,13, and 3,14beta1-4.  It
seems to be working in version 3.  This is fixed in 3.14beta5.  2
April 2004.

codonml (codeml for codons) in branch-site models (model = 2 NSsites =
2 or 3) prior to 3.14beta3 have a scaling problem, which makes the
length of the foreground branch to be incorrectly estimated.  Other
branch lengths and substitution parameters, such as the parameters in
the distribution, are corrected calculated, as well as the log
likelihood values and the posterior probabilities.  27 March 2004

pamp: The gamma parameter for variable rates among sites using the
method of Yang & Kumar (1996) is not estimated correctly in 3.14beta1,
beta2, beta3.  Versions 3.13d and earlier seem fine.

codonml (codeml for codons) in version 3.14beta and 3.14beta1 does not
work when fix_omega = 1 is used for branch models.  The results are
incorrect.  Please use newer versions 3.14beta3 or later.  Also
version 3.13 is fine.

baseml: Models TN93 and REV are wrong when used with Mgene = 3 or 4.
This seems correct in version 3.12 but went wrong in 3.13 and 3.14
since I inserted TN92 between HKY85 and TN93.  Thanks for Lee Bofkin
for reporting the error.

codonml (codeml for codons): When codon models are used to reconstruct
ancestral sequences (with RateAncestor = 1), the program lists
synonymous and nonsynonymous changes at each site under the heading
"Changes at sites (syn nonsyn)."  This listing is incorrect due to a
bug in the program.  This bug affects versions 3.12, 3.13 and 3.14,
and version 3.11 seems correct.  Thanks to Joe Bielawski.

baseml/codeml: The SE's for divergence times under the clock models
are calculated incorrectly.  This happens when you use clock = 1 or 2,
supply fossil date to calculate absolute times, and request standard
errors for times.  The estimates of times themselves are correct, but
standard errors for times are wrong.  The SEs for times and for the
rate under the TipDate model (clock = 3) are wrong as well.  The
programs print out the variances after the +-, instead of their square
roots.  This error was introduced in version 3.13.  Versions prior to
3.13 are correct.  I posted an update 3.13d to fix this bug.

evolver: the simulation program can now accept species names in the
tree.  Note that the data file formats for evolver (MCbase.dat,
MCcodon.dat, MCaa.dat) have changed and you might have to change your
own data files.  Look at the files included in the package.

The documentation in paml v3.13 from August 2002 - 12 December 2002
had a mistake about the critical values for the newer test using a
modified M8.  The critical values for the test are 2.71 at the 5%
significance level and 5.41 at the 1% level, rather than 1.95 and 3.32
as in the documentation.





Version 3.14beta2, November 2003

(1) baseml: Models TN93 and REV are wrong when used with Mgene = 3 or
    4.  This seems correct in version 3.12 but went wrong in 3.13 and
    3.14 since I inserted TN92 between HKY85 and TN93.  Thanks for Lee
    Bofkin for reporting the error.

(2) codonml (codeml for codons): When codon models are used to
    reconstruct ancestral sequences (with RateAncestor = 1), the
    program lists synonymous and nonsynonymous changes at each site
    under the heading "Changes at sites (syn nonsyn)."  This listing
    is incorrect due to a bug in the program.  This bug affects
    versions 3.12, 3.13 and 3.14, and version 3.11 seems correct.
    Thanks to Joe Bielawski.



Version 3.14beta, 20 July 2003

(1) baseml/codeml: rewrote likelihood clock and local clock models.
   Implemented models for combined analysis of multiple genes using
   multiple calibration points (Yang and Yoder 2003).  The option
   variable clock in the control files is now used differently from
   before.  See documentation below and also the readme and example
   files in the folder paml/examples/MouseLemurs/.

(2) codeml: added branch-site models C and D (Bielawski and Yang
   submitted).

(3) baseml/codeml: The SE's for divergence times under the clock
   models are calculated incorrectly.  This happens when you use clock
   = 1 or 2, supply fossil date to calculate absolute times, and
   request standard errors for times.  The estimates of times
   themselves are correct, but standard errors for times are wrong.
   The SEs for times and for the rate under the TipDate model (clock =
   3) are wrong as well.  The programs print out the variances after
   the +-, instead of their square roots.  This error was introduced
   in version 3.13.  Versions prior to 3.13 are correct.  I posted an
   update 3.13d to fix this bug.

(4) mcmctree: this program is decommissioned in this release.  The old
   program died and the new program is still under construction.

(5) evolver: the simulation program can now accept species names in
   the tree.  Note that the data file formats for evolver (MCbase.dat,
   MCcodon.dat, MCaa.dat) have changed and you might have to change
   your own data files.  Look at the files included in the package.

(6) Improved the iteration algorithm a little.  No change to the
   interface.

(7) The documentation in paml v3.13 from August 2002 - 12 December
   2002 had a mistake about the critical values for the newer test
   using a modified M8.  The critical values for the test are 2.71 at
   the 5% significance level and 5.41 at the 1% level, rather than
   1.95 and 3.32 as in the documentation.

(8) Edited the manual pamlDOC.pdf.




15 May 2003
paml3.13d

baseml/codeml: The SE's for times under the clock models are
calculated incorrectly.  This happens when you use clock = 1 or 2,
supply fossil date to calculate absolute times, and request standard
errors for times.  The estimates of times themselves are correct, but
standard errors for times are wrong.  The SEs for times and for the
rate under the TipDate model (clock = 3) are wrong as well.  The
programs print out the variances after the +-, instead of their square
roots.  

This error was introduced in version 3.13.  Versions prior to 3.13 are
correct.


12 December 2002 correction of documentation

The paml documentation in paml v3.13 from August 2002 - 12 December 2002
has a mistake about the critical values for the newer test using a
modified M8.

The critical values for the test are 2.71 at the 5% significance level
and 5.41 at the 1% level, rather than 1.95 and 3.32 as in the
documentation.  I made a mistake and quickly discovered it.  I thought
I corrected this a few months ago, but apparently the document
included in the paml release had this mistake.  I am sorry.  I'll
correct it now.



Version 3.13, August 2002

(1) baseml: nhomo = 1 and model = 6 (for both the one-rate and gamma-rates
    models) in version 3.12 gives incorrect results.  The error was introduced 
    in version 3.12 and is now fixed.  Sorry for the trouble and thanks to
    Joshua Scott Rest.

(2) baseml: Tamura's (1992) model is inserted between HKY85 and TN93.  
    Unfortunately this means that the model code for TN93 and REV are shifted, 
    and you have to change your control file for those two models.  I also 
    added user-specified REV or UNREST models.
    0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93,
    7:REV, 8:UNREST, 9:REVu; 10:UNRESTu

(4) I implemented the nonhomogeneous models of Galtier and Gouy
    (1998).  The options are model = 5 (T92) and nhomo = 3 (N1) or 4
    (N2) or 5 (user).  nhomo = 5 is added for the model of Yang and
    Roberts (1995) as well.  It means that the user specifies, in the
    tree, how many sets of base frequencies (or how many GC content
    parameters in the model of Galtier and Gouy 1998) should be used
    and which branches has which sets.

(5) codeml: For pairwise amino acid sequence comparison (seqtype = 2
    and runmode = -2), the program crashes.  This is fixed now.
    Thanks to Dennis Paul Wall.  

(6) codeml: The mechanistic models of amino acid substitution (model = 6 or 7)
    are broken for quite some time due to lack of maintenance.  I have
    now fixed them.  See the file examples/mtCDNA/readme.txt.

(7) codemlsites is now removed, which is for batch run of multiple NSsites
    models.  This is now done by specifying several NSsites models in
    the control file codeml.ctl for codeml, for example: NSsites = 0 1
    7 8.

(8) baseml & codeml used to ask the user what to do if the tree has branch 
    lengths.  I have now introduced a variable fix_blength in the control 
    file that does the same thing. 
    fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed



Version 3.12, March 2002

(1) baseml and codeml, Mgene=2 or 4 (different pi's) and RateAncestor
    = 1 Ancestral reconstruction does not work properly although the
    ML iteration is fine.  The output likelihood values (in the form
    "Node 20: lnL = -1047.965624") are different from the optimum
    likelihood already calculated.  The option was fine in version
    3.0e and 3.1, and was broken in version 3.11.

(2) codeml stops with an error message "pi=0" when some amino acids are 
    missing in the sequences.  Earlier versions of the program are correct.

(3) yn00 now accepts multiple data sets (specified by ndata).


Version 3.11, September 2001

(1) baseml and codeml (clock = 1 or clock = 2) sometimes print out
    ridiculous (e.g., large negative) tree lengths and branch lengths.
    I thought this was fixed in version 3.1, but it was not.
    Hopefully it is now fixed.

(2) baseml and codeml: Malpha (a separate alpha for each site
    partition) does not work with Mgene = 0.  The output will give you
    the same alpha value for each gene as you specify in the control
    file.  This is now fixed.

(3) baseml: When the REV or UNREST models (model = 6 or 7) are used
    together with Mgene = 2, 3, 4, the program outputs one Q matrix,
    when each site partition should have a different Q matrix.  The ML
    parameter estimates are correct, but I did not bother to format
    the output correctly.  The single Q matrix in the output is the
    one for the first partition.  I have added the output for the
    other matrices now.

(4) baseml and codeml.  Ancestral reconstruction was disabled for
    large trees with more than 100 or 200 sequences in previous
    versions.  It is now allowed.  On large trees, the multiplication
    of transition probabilities across branches in the tree cause the
    product to become too small to be represented in the computer.
    This is known as underflows.  I implemented a scaling algorithm to
    avoid underflows some time ago but did not bother to do it with
    the ancestral reconstruction algorithm at the time.  The algorithm
    should now work, up to the upper limit set in the program, that
    is, 1000 or 2000 sequences.



Version 3.1, June 2001

Changed the way of counting base or amino acid frequencies so that
this version of baseml or codeml might generate different results from
previous versions under the following model specifications.  

   . baseml & aaml: if you have multiple genes and the model uses the same
   frequencies in the model for the different site partitions.  

   . codonml:
   if you have ambiguity characters at all.  Ambiguity characters were
   ignored when counting frequencies in previous versions but are used now.

There is no difference if your data do not contain any alignment gaps
or ambiguity characters or if you choose to remove them before any
analysis (cleandata = 1).  The early versions used two ad hoc methods
in dealing with such ambiguity characters in different places of the
programs.  The new version uses another ad hoc method and in all
places.  I think it will be fine which ever version you use, but do
not use different versions in the same analysis.

codonml (codeml with seqtype = 1) with Mgene = 1 does not work
correctly if the sequences have alignment gaps or ambiguity
characters.  Mgene = 1 means separate analysis.  The bug causes data
for the genes except the first to be read out of frames, so that most
likely you will see a lot of messages "stop codon XXX" before the
program aborts.  This is now fixed.


codonml (codeml with seqtype = 1) with fix_alpha=0: In the final
output for the codon + gamma model, parameter alpha is not correctly
identified.  If you have fix_kappa = 0, fix_omega =0, and fix_alpha=0,
the last three numbers should be kappa, omega (dn/ds), and alpha.  The
detailed output did not identify alpha correctly, although the
likelihood value and the outputted rates and frequencies (r and f) are
correct.  I believe this is now corrected.



Version 3.0e, 14 May 2001

codonml (codeml with seqtype = 1) with model = 1: The program crashes
when you have a small tree with <= 5 branches.  This is a new error
introduced in version 3.0c.  It is now fixed.

baseml and codeml (clock = 1 or clock = 2) sometimes print out ridiculous
tree lengths and branch lengths.  

yn00 in version 3.0c ignores icode and uses the universal code only.
It was correct in vesion 3.0b.  This is fixed in version 3.0d.


Versions 3.0c-3.0d, 20 February 2001

We bought a Pentium III cluster running redhat linux 6.2.  The gcc
compiler 2.61 seems to have bugs and codeml does not run for NSsites =
7 or 8.  The program might output "points out of order" or "Det goes
to 0" error messages.  3.0d seems to be safer for these models.

codonml (codeml with seqtype = 1) with NSsites = 3 might generate a
message "error: sortwM3." and then stop with no output after the
iteration.  This is now fixed.  During the iteration, there was no
restriction on the w values, so that w0 can be greater than w1 and so
on.  At the end of the iteration, I sort the three w values so that w0
< w1 < w2 before outputting.  3.0c has a bug at sorting.  If you don't
see the error message, everything is fine.


10 November 2000

The probabilities for Joint ancestral reconstruction are not correct.
Many values are larger than 1.  Fixed in version 3.0c.



Version 3.0c, 30 October 2000

(1) Changed parameterization of clock models (clock = 1, 2, or 3), so that
the output now lists node ages, and the SEs are for node ages as well.
Node ages are measured by the expected number of nucleotide or amino
acid substitutions per site (nucleotide, amino acid, or codon) from
the node to the present time, and are proportional to the divergence
times.  In earlier versions, the output list proportions.

(2) codonml: problem with NSsites model with multiple gene data
(Mgene=1) is now fixed(?).  In the earlier version, the likelihood
calculation was o.k., but identification of sites under positive
selection was incorrect as the program attempted to list sites in
another gene when it was analyzing data for one gene.  (1) Mgene
options for codons and amino acids:



Version 3.0b, 6 October 2000

The local clock models (clock = 2) are not implemented correctly in paml3.0 or 3.0a. 

Yoder, A. D., and Z. Yang.  2000.  Estimation of primate speciation
dates using local molecular clocks.  Molecular Biology and Evolution
17 (7): 1081-1090.

I introduced a serious error before I made the models available to the
public, in ver3.0 (May 2000).  Two symptoms are noted right now: (1)
crashes (which are good as they make you realise that something is
wrong immediately) and (2) the local clock model (clock=2) having a
worse likelihood than the global clock model (clock = 1).  The results
in the paper are correct except for a typo ("37.30 - 48.48" in table 3
for the cetacean-whale divergence using the C3 calibration should be
"57.30 - 48.48").  I now include the example data sets and results
from that paper to help you prepare your own data files.

Sorry for any damages done.

Many thanks to Toby Johnson and Philip Awadalla for spotting the error.



Version 3, 4 February 2000

The program evolver may not generate sequences correctly if branch
lengths are very large, say >10.  

Scaling by nodes to avoid underflow.  When there are many sequences in
the data (say > 200 or 300), the probability of observing data at a
site can become too small to represent in the machine.  This is
because the probabilities are multiplied along branches in the tree
and a large tree has many branches.  Since version 2.0, this underflow
is dealt with by scaling, and it works with both the one-rate and
gamma-rates models.  It did not work with the NSsites models in
codonml, but probably nobody has analysed large data sets to notice
this.  Anyway, this version hopefully fixes that problem, when I was
analysing the data set of Bush et al. (1999 MBE 16:1457-1465), which
has about 350 sequences.  If you use the program on very large data
sets, watch out for anything strange and let me know.  I suppose with
the option of using supplied branch lengths, data sets of such sizes
will become manageable, and this scaling will become important.



Version 2.0h, Oct 14, 1999

Fixed the following errors, all simple errors.

The RemoveIndel routine in 2.0e and 20.f has a bug that removes most
sites in the sequence except those with all T's and C's for baseml.
The same routine in 2.0g has a different bug that removes most sites
except those will all T's and C's in the sequence for aaml.  In either
case, the results will be grossly wrong.  The bugs affect the analysis
only if you have gaps or ambiguity characters in the data and use
runmode = 1 for aaml in 2.0e and 2.0f, and runmode = 1 for codonml for
2.0g.

The newly introduced option for amino acid reconstruction by baseml
(icode) does not work.  The program aborts with an error message.
This is now fixed.




Version 2.0g, Sept 21, 1999

Fixed a bug in 2.0f that causes crash in codeml when getSE = 1.  

If the tree has branch lengths, codeml and baseml in 2.0f will simply
use the branch lengths rather than estimating them by iteration.  I
have added a question for the user to choose to ignore the branch
lengths, use them as fixed or use them as initial values for the
iteration.



Version 2.0d, June 30, 1999
Fixed some convergence problems in ML pairwise estimation of dS and 
dN, in particular, in presence of data partitions (the G option).

Fixed a bug in evolver.  The bug means that no sensible data are
generated if the tree has branch lengths smaller than 1e-7.  At some
point, I did something "clever" (taking advantage of the fact that at
such small branch lengths, no evolution would occur), which destroyed
the calculation.  



Version 2.0c, May 12, 1999
Corrected a few problems with the evolver program, and with running 
multiple data sets using baseml.  Added REV in MCbase.dat.
Thanks to John Mercer.

Note--Uncomment ndata in baseml or codeml to analyse multiple
data sets generated from evolver.



April 16, 1999

Although posted only a few days ago, paml2.0 has an error in the
program codeml, which invalidates most analyses based on codon
substitution models.  The symptom is relatively easy to spot and is
indicated by one of the parameters (say omega) not being estimated at
all and in the output you will have exactly the same number as you
specified in the control file.

Amino acid-based analysis or pairwise comparison of codon sequences
are not affected.  Use paml2.0a to redo the analysis.  Apologies for
the trouble.



version 2.0, 31 March 1999
Added back the faster calculation when there is no missing data.
Enabled the programs/analysis that broke in the temporary versions, 
such as pamp, joint reconstruction.

Renamed listtree as evolver, and added simulation options.



PAML 1.4 Temporary versions
Dec98 & Jan99 

  pamlTMP.Jan99.notes
  ===================
  Ziheng Yang
  Fri Jan 15 10:01:42 GMT 1999

  .Type make to compile the programs.  If you got error messages, see
  whether you know how to change the file Makefile.  If it does not work
  either, look at the files paml.cc, paml.gcc, etc.

  .At the suggestion of David Posada, I added ML estimation of pairwise 
  distances between amino acid sequences in the program codeml.  

  The relavant variables in the control file codeml.ctl are 

   runmode = -2 for pairwise distance calculation
     aaRatefile = jones.dat * only used for aa seqs with model=empirical(_F)
              * dayhoff.dat, jones.dat, mtmam.dat, or your own
     model = 3 
     alpha = 0

  model specifies the amino acid substitution model.  You should choose
  a value from 0, 1, 2, 3.  If you want to estimate the rate matrix from
  your data, you should do that using many sequences and then move the
  estimated substitution rate matrix (in the output file mlc) into a
  file and change the variable aaRatefile.  

  Choosing alpha>0 means using gamma distance with that specified alpha
  parameter.  If you see anything strange, please let me know.

  .I have included only three programs baseml, codeml, and listtree.
  I have not tested the others and so they are not included.



  pamlTMP.Dec98.notes
  ===================
  Ziheng Yang
  Wed Dec  9 10:44:37 GMT 1998


  This temporary version of paml has involved a number of changes, and
  is quite likely to contain errors.  Please let me know if you notice
  anything strange.  Some of the options do not work for now.  Details
  follow.  I will compile the Win32 and PowerMac versions after
  everything is fixed and tested.

  . Missing data: baseml and codeml now handle missing data.  Choose
  DelMissing = 1 in the control file to remove sites with ambiguity
  characters or alignment gaps, as did previous versions.

  . Clock: The clock is now fixed.  It may still crash, but the option
  is not worse than the no-clock options.  The definitions of the node
  times or branch lengths are now different from the documentation
  (pamlDOC.html), and so check the branch lengths in the output tree
  topology.  Thanks to Jeff Thorne.

  . Nexus file formats: Paml programs now read sequence files and tree
  structure files in the Nexus format used by paup and MacClade.  Only
  the data or tree are read, and everything else in the file is ignored.

  .  Ancestral reconstruction: Marginal ancestral reconstructions are
  now done under the gamma-rates model as well as the constant-rate
  model.  For protein-coding genes, reconstructions can now be done at
  the nucleotide level with baseml (in particular, by using models that
  account for differences at the three codon positions), at the amino
  acid level with aaml, and at the codon level with aaml.  According to
  Belinda Chang, those different reconstructions tend to be similar.
  Results for ancestral reconstruction are now listed by site, and not
  by site pattern as in earlier versions.  Missing data are now handled
  in those analysis.  See instructions in this doc about baseml.ctl for
  more options.  Thanks to Belinda Chang.  I would like to take this
  opportunity to point out that the reconstructed ancestral sequences
  are not the real observed sequences and may contain errors.

  . I have disabled the option for variable rates among sites in
  combination with variable dN/dS rate ratios among lineages in codonml.
  This option has never been implemented in the program but was not
  disabled.

  . Distance matrices from codonml.  The program codonml outputs
  matrices of synonymous and nonsynonymous rates in all pairwise
  comparisons using the method of Nei & Gojobori (1986) into two files
  named DistanceNG.dN & DistanceNG.dN.  The matrices are lower-diagonal
  and can be used with programs, such as neighbor and fitch, in phylip
  (and possibly paup* too) for tree reconstruction or branch length
  estimation by distance methods.  If you choose runmode = -2 for ML
  pairwise comparison, the program will also output two matrices of ML
  estimates into two files named DistanceML.dS & DistanceML.dN, for
  synonymous and nonsynonymous rates.  Since many users seem interested
  in looking at dN/dS rate ratios among lineages, examination of the
  tree shapes indicated by branch lengths calculated from the two rates
  may be interesting although the analysis is intuitive.  Obviously, you
  should NOT name your own data files with those names; otherwise they
  will get overwritten.  If your species name has more than 10
  characters, you will have to edit the files and cut the names short
  before you can use Phylip programs.  I have decided to leave this work
  to the user.  I plan to create some other distance matrix files for
  nucleotides and amino acids as well.

  . An minor prompt error when running codonml with model = 2 (variable
  dN/dS ratios among lineages) is fixed.  The example data set
  lysozymeSmall.nuc is included for the user to duplicate my results in
  Yang (1998 Molecular Biology and Evolution 15: 568-573).  The control
  file codemlLysozyme.ctl explains in more detail how to specify the
  options.  I would like to remind you that it is not correct to use the
  option model = 1 to estimate dN/dS ratios for branches to find out
  which ratios are greater than one, and then to use model = 2 to test
  whether that ratio is significantly greater than one.  The problem
  with such an analysis is that the hypothesis being tested is derived
  from the data which you use to test the hypothesis, and as a result,
  you tend to get significantly results too often.  Strictly speaking,
  the hypothesis should be formulated before the data are analysed.

  Things that do not work in this version include

  . All parsimony-based analyses are now broken.  The program pamp is
  not included.  Programs baseml and codeml used to calculate the MP
  score for each tree before doing an ML analysis on that tree.  Now a
  -1 is used to indicate this is not possible.



Version 1.4 (UCL)
July 1998 

     1. Most of the changes are in the program codeml (aaml for amino
  acid sequences and codonml for codon sequences). A few new models of
  codon substitution are implemented (see Yang and Nielsen 1998; Nielsen
  and Yang 1998; Yang 1998).
     2. Some problems relating to ancestral sequence reconstruction (in
  baseml and codeml) are fixed. The earlier algorithm does not work
  properly if the data contain more than several sequences. The
  algorithm makes a guess at the likely character states at the interior
  nodes of the tree, and then uses those to generate reconstructions
  (joint reconstructions, see eq. 2 in Yang et al. 1995) to be
  evaluated. Sometimes this strategy misses important reconstructions,
  and as a result, the probabilities for reconstructed characters at
  specific interior nodes (marginal reconstructions; see eq. 4 in Yang
  et al. 1995) are substantially underestimated if the number of
  sequences is not very small. I have now written separate codes to do
  the marginal reconstruction, evaluating all possible character states
  for each interior node. This works also under the gamma model of
  substitution rates among sites, a feature that was not implemented
  before. The joint reconstruction works with one rate for all sites
  only and has the old problem of possibly missing important
  reconstructions. However, the posterior probabilities for those joint
  reconstructions that do get evaluated are accurate. I have added an
  option (choose RateAncestor = 2 rather than 1) for the user to specify
  the reconstruction to be evaluated. The two approaches are expected to
  produce very similar results, and since the marginal reconstruction is
  always reliable, perhaps it can always be used for data analysis.
  (Thanks to Belinda Chang.)
     3. The output file for estimated rates for sites under the
  variable-rates models is now "Rates.out" instead of "rst".
     4. I have implemented ancestral sequence reconstructions based on
  codon-substitution models (codonml). This has not been tested
  carefully, and I would appreciate your comments if you use it.
     5. A number of minor changes have been made. I have fixed several
  floating exception errors that seem to occur on DEC Alpha machines
  only.
     6. The documentation is now changed into the html format. 



Version 1.3a,b,c (UCL)
June 1998 

  1. Basemlg was put back at the request of a user.

  2. Some changes are made to codeml concerning codon-substitution
  models (Yang and Nielsen 1998 JME; Yang 1998 MBE; Nielsen and Yang
  1998 Genetics)



PAML Version 1.3: (UC Berkeley)
July 1997 

  1. Starting with this version, the program basemlg will not be
  included in the package.  This program implements the (continuous)
  gamma model of substitution rate variation among nucleotide sites
  (Yang 1993).  It involves intensive computation and has been
  superseded by the discrete-gamma model implemented in the program
  baseml.  If you want to use this program, you should use previous
  versions of paml, which can be obtained from me if nowhere else.

  2. The simulation program mcml.c is removed from the package.  This is
  now superced by the program listtree.c, which does different things
  besides simulating data sets.

  3. I have implemented the stepwise addition algorithm in the programs
  baseml and codeml.  This algorithm is faster than the
  star-decomposition algorithm implemented before, but my implementation
  is crude and inefficient.  The NNI perturbation is implemented too.
  These work without the molecular clock.

  4. Many changes are made with the program codonml (codeml with
  seqtype=1).  A few new codon-based models are implemented.  One
  assumes different nonsynonymous/synonymous (dN/dS) rate ratios among
  branches in the phylogeny, and may be useful for detecting episodic
  positive selection.  Another allows the dN/dS ratio to vary among
  sites and may be useful for testing neutrality and detecting
  positively-selected sites in the sequence.  These are based on my
  collaborative work with Rasmus Nielsen.  I made some changes to the
  output of estimates of dS and dN in pairwise comparisons (codonml with
  runmode=-2), so that the results are easy to understand.  Another
  change with this program is in the codon-substitution model of Goldman
  and Yang (1994).  We used the amino acid distance matrix of Grantham
  (1974) to modify the rate of nonsynonymous substitutions, but
  unfortunately the model does not fit data well.  It does not always
  fit the data better than if we simply assume equal distance between
  any two amino acids.  So I have added the option of ignoring the amino
  acid differences.  Goldman and Yang's original formula is still
  available but not recommended for use.  As a result of these changes,
  the formulation of the Goldman and Yang model is now somewhat
  different from the paper and previous versions of the program.  See
  Section 6.2 for details.

  5. I have again made some changes with the user interface, based on my
  guess of what the "user" would like to see.



Version 1.1a-d: (University of California, Berkeley)
1995-1996 

1.1a No records of changes remain.

1.1b November, 1995:

The following line at the beginning of the file tools.h 
      #define __cplusplus
is removed.  I added this line to avoid some (unjustified) warning
messages from a compiler I used to use and forgot to remove it when I
was preparing paml1.1.  This line made some compilers unable to
compile.

A bug that caused baseml and basemlg to give wrong estimates of kappa
under the F84 model is now fixed.  Estimates of kappa under the F84
models listed in the paml 1.0 and 1.1 documents are all incorrect and
are a bit too small.  For example, the estimate of kappa under the F84
model for the mtDNA data of Brown et al. (1982) should be 4.344 while
the wrong estimate given in the large table of the document is 3.420.
Likelihood value, branch lengths and other parameters seem to have
been correctly calculated by paml 1.0 and 1.1.  Versions prior to 1.0
do not have this bug, and results in Yang (J. Mol. Evol. 1994,
39:306-314) and Yang, Lauder, and Lin (J. Mol. Evol. 1995,
41:587-596), where the F84 model was used, are correct.

1.1c March 1996 

Representation of tree topologies using branches (see the document)
are now allowed (restored) in the tree structure file.  This is for
coping with cases where some taxa are ancestors of others.  If this
representation is used, the line starts with a dollar sign.  So the
following line in the file trees.5s (the tree file for 5 species)

$ 5      6 3  6 4  6 5  3 1  3 2

represents the tree ((12)34), with 5 to be the ancestor of 1 and 2.

Alignment gaps are now allowed when option G is used (for multiple
genes).  The gaps are removed before analysis.

A small program listtree lists all the bifurcating trees for a given
(small) number of species.

codonml (codeml.c with seqtype=1) now has an option for calculating
the number of synonymous substitutions per synonymous site (Ks) and
the number of nonsynonymous substitutions per nonsynonymous site (Ka)
and their ratio for each pairwise comparison, using the method of
Goldman and Yang (1994).  This is implemented with
runmode=-2. Estimates of Ks and Ka are collected in the file rst and
estimates of model parameters in the file mlc.  This option produces
table 2 in the Goldman & Yang paper.

The interior nodes were incorrectly identified when the ancestral
sequences were listed in the file rst.  They were all one less than
their correct numbers.  Nodes 7, 8, 9, 10 for the stewart.aa data were
incorrectly identified as nodes 6, 7, 8, 9.  This is corrected now.

1.1d. July 1996

An unintended version of codeml.c was included in version 1.1c, which
causes the program to produce different results under the codon-based
model of Goldman and Yang (1994).  The small number in baseml.c was
set too small, making the program do unnecessary iterations; this is
fixed now.  I also changed the program pamp so that it will estimate
the substitution rate matrix without using a tree.

I have included a few other genetic code tables in this version of
codeml; see the file codeml.ctl.


PAML Version 1.2: November 1996 (UC Berkeley)

  1. I have done some changes with the user interface.  Name of files
(sequence data file, control file, tree structure file) are now
specified in the control files (The default are baseml.ctl,
codeml.ctl, pamp.ctl, mcmctree.ctl).  The command line for executing a
program is now ProgramName ControlFileName with ControlFileName
optional.  I have added some text in the output file of baseml so that
the results are eassier to understand.  Choose verbose=0 in the
control file if you do not want the detailed output.

  2. A new program mcmctree is included, which performs Bayesian
estimation of phylogenies using Markov chain Monte Carlo methods
(Rannala and Yang 1996; Yang and Rannala 1997).

  3. A number of minor changes are made, such as using species names
in the parenthesis tree representation.



July 1995 
Version 1.1: (IMEG PennState)

  Models for analyzing data of multiple genes (Yang 1996 JME) are
  implemented in baseml and codeml.  Two more programs are included:
  pamp for parsimony-based analysis implementing the methods of Yang and
  Kumar (1996 MBE) and mcml for Monte Carlo simulation (prepared for
  Arndt von Haeseler but apparently not used).


February 1995 
Version 1.0 (IMEG, PennState)

  This is the first official version of paml.  Three main programs are
  included: baseml, basemlg and codeml.  Control files are used for all
  of them.  The program codeml is formed by merging two programs codonml
  and aaml, for codon sequences and amino acid sequences, respectively.
  One rate, gamma rates, and auto-discrete-gamma rates for sites are
  implemented for nucleotide, amino acid, and codon-based models.  The
  document is provided as postscript files (paml1_3.ps).


October 1994 
Version 0.12, no name for package (BAU and IMEG PennState) 

  The bracket notation of tree topologies is introduced.  Tree
  search by star decomposition is implemented in baseml and codonml.
  The options for baseml are moved into an option file baseml.ctl.  The
  molecular clock seems to work with the automatic tree search model
  (runmode=1 or 2).  The old readme file is renamed manual.


March 1994 
Version 0.10, no name for package: (NHM, England)

  Programs tripml and comptree are renamed codonml and rell.  The readme
  file is expanded and the numerical optimization routine, ming1, used
  by dnaml and codonml, is improved.  The discrete-gamma model of Yang
  (1994 JME) is implemented in both baseml and codonml.

  Preliminary version 0.11, no name for package: April 1994 (NHM,
  England) Programs dnaml and dnamls are renamed baseml and basemlg to
  avoid confusion with Joe Felsenstein's programs.  The
  auto-discrete-gamma model and the nonparametric models of rate
  variation and correlation mong sites of Yang (1995 Genetics) are added
  in baseml.  Nonhomogeneous-process models of Yang and Roberts (1995
  MBE) are implemented in baseml.


April 1993 
Version 0.01, no name for package (Cambridge).  Three programs are included in 
the package:

  1. dnamls implements the model of gamma rates among sites of Yang
  (1993) and works with arbitrary topologies and substitution models
  (JC69, K80, F81, HKY85).

  2. dnaml implements the model of a single rate for all sites. (The
  same name as Joe Felsenstein's program was used.)

  3. tripml implements the codon-based model of Goldman and Yang (1994).
  Trees are represented by the "branch notation".

// end of file
