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Port Changes: - Add EXAMPLES option and install most files under EXAMPLESDIR - Add USES=dos2unix to fix DOS line endings Upstream Changes: Version 4.9h, March 2018 (*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for rates for loci. Since 4.9d, the program and the documentation are inconsistent about the two priors, and which value (0 or 1) means which prior. I have now checked the program and the documentation to make sure that they are consistent: prior = 0: gamma-Dirichlet (dos Reis 2014). This is the default. prior = 1: conditional i.i.d. prior (Zhu et al. 2015). I believe these two are similar especially if the number of loci (partitions) is large, but no serious comparisons between the two priors have been published. Thanks to Adnan Moussalli for pointing out the errors. (*) codeml. It was discovered that the mechanistic amino acid substitution model implemented in Yang et al. (1998; see table 3), specified by seqtype = 2 model = 6, has been broken for a long time, since version 3.0 (2000) at least. Version 2.0 (1999) seems to be correct. This means that the model become broken soon since it was published. I have now fixed this. This model of amino acid substitution starts from a Markov chain for codons and then aggregate the states and merge the synonymous codons into one state (the coded amino acid). This is an approximate formulation since the process after state aggregation is not Markovian anymore. I have now added another codon-based amino acid substitution model that treats amino acids as ambiguities codons. The model is specified by seqtype = 2 model = 5. This is an exact formulation. (*) codeml. The number of categories in the BEB calculation under M2 and M8 is unintentionally set to 4 rather than 10. I have changed this back to 10. The details of this calculation are in Yang et al. 2005 MBE. Version 4.9g, December 2017 (*) codeml. A bug caused the BEB calculation under the site model M8 (NSsites = 8) to be incorrect, with the program printing out warming messages like "strange: f[ 5] = -0.0587063 very small." This bug was introduced in version 4.9b and affects versions 4.9b-f. A different bug was introduced in version 4.9f that causes the log likelihood function under the site model M8 (NSsites = 8) to be calculated incorrectly. These are now fixed. Version 4.9f, October 2017 (*) baseml, nonhomogeneous models (nhomo & fix_kappa). Those models allow different branches on the tree to have different Q matrices. Roughly nhomo controls the base frequency parameters while gix_kappa controls kappa or the exchangeability parameters (a b c d e in GTR/REV, for example). I added the option (nhomo = 5, fix_kappa = 2), which lets the user to define branch types, so that branches of the same type have the same exchangeability parameters (a b c d e for GTR) and base composition parameters, while branches of different types have different parameters. Branch types are labeled (using # and $), 0, 1, 2, .... The labels should be consecutive positive integers. The old options nhomo = 3 or 4 work for some models like GTR, but not some other models which also have base composition parameters. In this update, I think those options should work with all those models. I have also edited the documentation (look for option variable nhomo for baseml). (*) baseml & codeml. i added an option fix_blength = 3 (proportional), which means that branch lengths will be proporational to those given in the tree file, and the proportionality factor is estimated by ML. (*) codeml. The program does not count the parameters correctly for model M0 when fix_kappa = 1. The bug was introduced in version 4.9c and affects versions 4.9c-e. This is now fixed. (*) codeml (seqtype = 2 model = 2). If you are analyzing multiple protein data sets (ndata > 1) 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, etc. A bug in the program means that for the second and later data sets, the equilibrium amino acid frequencies are taken from the real data and not correctly set to those specified by the empirical models. I note that this bug was recorded in the update Version 3.14b, April 2005, but it was somehow not fixed, even in that version. This is now fixed. Thanks to Nick Goldman for reporting this again. (*) evolver (options 5, 6, 7 for simulating nucleotide, codon and amino acid alignments). If you choose 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), and if you are simulating two or more alignments, the program crashes after finishing the first alignment. This is now fixed. (*) mcmctree. The program crashes if you have a mixture of morphological loci and molecular loci, if not all the morphological loci are before the molecular loci. I have now fixed this. I think this was never described anyway. Version 4.9e, March 2017 (*) Edited the readme files to change the license to GPL. (*) mcmctree. A bug was introduced in version 4.9b which causes the program to read the fossil calibration information in the tree file incorrectly, if joint (minimum and maximum) bounds are specified using the symbol '<' and '>'. If you use the notation "B()", "L()", and 'U()', the information is read correctly. This bug was introduced in version 4.9b and exists in 4.9c and 4.9d. Versions 4.9a and earlier were correct. Version 4.9d, February 2017 (*) 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).
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142 B
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4 lines
142 B
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TIMESTAMP = 1524675240
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SHA256 (paml4.9h.tgz) = 623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3
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SIZE (paml4.9h.tgz) = 6241149
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