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mirror of https://git.FreeBSD.org/ports.git synced 2025-01-17 08:01:36 +00:00
freebsd-ports/biology/paml/pkg-plist
Joseph Mingrone 4fb4ec21f6 biology/paml: Update to version 4.9i
Upstream changes as described by the author:

- 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.
2019-02-26 15:12:42 +00:00

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%%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf
%%PORTDOCS%%%%DOCSDIR%%/README.txt
%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/6s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/9s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/ECP_EDN_15.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/PAMLCladeModelCDnotes.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeC.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeD.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/tree.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BF.Clock23.xlsx
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BFdriverDOC.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/FixedDsClock23.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.BayesFactor.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf1/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf2/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.Infinitesites.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri123.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/GeneticCode.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs123.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README2.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/mtmam.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/eigenQREV.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/testPMat.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranches.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSclade.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSsites.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/PositiveSites.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.Nulldata.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.NodeNumbers.tre
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.nexus
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.tre
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/commands.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/in.BV.HKYG5
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/FigTree.tre
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/baseml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.rooted.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codonml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dNdSGene1.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/MtZoa.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV10.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV64.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff-dcmut.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974a.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974c.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974p.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974v.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/grantham.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones-dcmut.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/lg.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/miyata.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtArt.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/RasMol.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/SiteNumbering.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codemlYangSwanson2002.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysinYangSwanson2002.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcmctree.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/AAcodon.result.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.AAcodon.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/miyata.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/2s.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/OmegaAA.dat
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.HC.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNA.HC.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupstart
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl
bin/baseml
bin/basemlg
bin/chi2
bin/codeml
bin/evolver
bin/evolverNSbranches
bin/evolverNSbranchsites
bin/evolverNSsites
bin/pamp
bin/yn00