The following packages will be installed: paml Fetching LICENSE... 0%100%100%100%100%100%Done Fetching README... 0%100%100%100%100%100%Done Fetching References... 0%100%100%100%100%100%Done Fetching paml.SlackBuild... 0%100%100%100%100%100%Done Fetching paml.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done paml4.9j/ paml4.9j/3s.trees paml4.9j/4s.trees paml4.9j/5s.trees paml4.9j/6s.trees paml4.9j/GeneticCode.txt paml4.9j/MCaa.dat paml4.9j/MCbase.dat paml4.9j/MCbaseRandomTree.dat paml4.9j/MCcodon.dat paml4.9j/README.txt paml4.9j/Technical/ paml4.9j/Technical/Pt/ paml4.9j/Technical/Pt/eigenQREV.pdf paml4.9j/Technical/Pt/testPMat.c paml4.9j/Technical/Simulation/ paml4.9j/Technical/Simulation/Codon/ paml4.9j/Technical/Simulation/Codon/MCcodonNSbranches.dat paml4.9j/Technical/Simulation/Codon/MCcodonNSbranchsites.dat paml4.9j/Technical/Simulation/Codon/MCcodonNSclade.dat paml4.9j/Technical/Simulation/Codon/MCcodonNSsites.dat paml4.9j/Technical/Simulation/Codon/PositiveSites.c paml4.9j/Technical/Simulation/Codon/PositiveSitesBEB.exe paml4.9j/Technical/Simulation/Codon/PositiveSitesBS.exe paml4.9j/Technical/Simulation/Codon/PositiveSitesNEB.exe paml4.9j/Technical/Simulation/Codon/README.txt paml4.9j/Technical/Simulation/Codon/codeml.ctl paml4.9j/Technical/Simulation/Codon/evolverNSbranches.exe paml4.9j/Technical/Simulation/Codon/evolverNSbranchsites.exe paml4.9j/Technical/Simulation/Codon/evolverNSsites.exe paml4.9j/Technical/Simulation/multiruns.c paml4.9j/Technical/Simulation/multiruns.exe paml4.9j/Technical/Simulation/multiruns.txt paml4.9j/aaml.ctl paml4.9j/baseml.ctl paml4.9j/bin/ paml4.9j/bin/baseml.exe paml4.9j/bin/basemlg.exe paml4.9j/bin/chi2.exe paml4.9j/bin/codeml.exe paml4.9j/bin/evolver.exe paml4.9j/bin/infinitesites.exe paml4.9j/bin/logoMCMCtree_MAC.jpg paml4.9j/bin/mcmctree.exe paml4.9j/bin/pamp.exe paml4.9j/bin/yn00.exe paml4.9j/brown.nuc paml4.9j/brown.rooted.trees paml4.9j/brown.trees paml4.9j/codeml.ctl paml4.9j/codonml.ctl paml4.9j/dat/ paml4.9j/dat/MtZoa.dat paml4.9j/dat/cpREV10.dat paml4.9j/dat/cpREV64.dat paml4.9j/dat/dayhoff-dcmut.dat paml4.9j/dat/dayhoff.dat paml4.9j/dat/g1974a.dat paml4.9j/dat/g1974c.dat paml4.9j/dat/g1974p.dat paml4.9j/dat/g1974v.dat paml4.9j/dat/grantham.dat paml4.9j/dat/jones-dcmut.dat paml4.9j/dat/jones.dat paml4.9j/dat/lg.dat paml4.9j/dat/miyata.dat paml4.9j/dat/mtArt.dat paml4.9j/dat/mtREV24.dat paml4.9j/dat/mtmam.dat paml4.9j/dat/wag.dat paml4.9j/doc/ paml4.9j/doc/MCMCtree.Tutorials.pdf paml4.9j/doc/pamlDOC.pdf paml4.9j/doc/pamlFAQs.pdf paml4.9j/doc/pamlHistory.txt paml4.9j/examples/ paml4.9j/examples/9s.trees paml4.9j/examples/CladeModelCD/ paml4.9j/examples/CladeModelCD/ECP_EDN_15.nuc paml4.9j/examples/CladeModelCD/PAMLCladeModelCDnotes.pdf paml4.9j/examples/CladeModelCD/codeml.CladeC.ctl paml4.9j/examples/CladeModelCD/codeml.CladeD.ctl paml4.9j/examples/CladeModelCD/tree.txt paml4.9j/examples/DatingSoftBound/ paml4.9j/examples/DatingSoftBound/BF.Clock23.xlsx paml4.9j/examples/DatingSoftBound/BFdriverDOC.pdf paml4.9j/examples/DatingSoftBound/FixedDsClock23.txt paml4.9j/examples/DatingSoftBound/README.BayesFactor.txt paml4.9j/examples/DatingSoftBound/README.txt paml4.9j/examples/DatingSoftBound/bf1/ paml4.9j/examples/DatingSoftBound/bf1/mcmctree.ctl paml4.9j/examples/DatingSoftBound/bf2/ paml4.9j/examples/DatingSoftBound/bf2/mcmctree.ctl paml4.9j/examples/DatingSoftBound/mcmctree.Infinitesites.ctl paml4.9j/examples/DatingSoftBound/mcmctree.ctl paml4.9j/examples/DatingSoftBound/mtCDNApri.trees paml4.9j/examples/DatingSoftBound/mtCDNApri123.txt paml4.9j/examples/HIVNSsites/ paml4.9j/examples/HIVNSsites/HIVenvSweden.trees paml4.9j/examples/HIVNSsites/HIVenvSweden.txt paml4.9j/examples/HIVNSsites/HIVenvSweden4s.trees paml4.9j/examples/HIVNSsites/HIVenvSweden4s.txt paml4.9j/examples/HIVNSsites/README.txt paml4.9j/examples/HIVNSsites/codeml.ctl paml4.9j/examples/MHC.Swanson2002MBE/ paml4.9j/examples/MHC.Swanson2002MBE/README.txt paml4.9j/examples/MHC.Swanson2002MBE/bigmhc.phy paml4.9j/examples/MHC.Swanson2002MBE/bigmhc.trees paml4.9j/examples/MHC.Swanson2002MBE/codeml.ctl paml4.9j/examples/MouseLemurs/ paml4.9j/examples/MouseLemurs/MouseLemurs.aa paml4.9j/examples/MouseLemurs/MouseLemurs.nuc paml4.9j/examples/MouseLemurs/MouseLemurs.trees paml4.9j/examples/MouseLemurs/MouseLemurs123.nuc paml4.9j/examples/MouseLemurs/README.txt paml4.9j/examples/MouseLemurs/README2.txt paml4.9j/examples/MouseLemurs/aaml.ctl paml4.9j/examples/MouseLemurs/aaml2.ctl paml4.9j/examples/MouseLemurs/baseml.ctl paml4.9j/examples/MouseLemurs/baseml2.ctl paml4.9j/examples/MouseLemurs/codeml.ctl paml4.9j/examples/MouseLemurs/codonml.ctl paml4.9j/examples/MouseLemurs/codonml2.ctl paml4.9j/examples/MouseLemurs/mtmam.dat paml4.9j/examples/README.txt paml4.9j/examples/TipDate.FluH1/ paml4.9j/examples/TipDate.FluH1/H1.Beast.Nulldata.xml paml4.9j/examples/TipDate.FluH1/H1.Beast.xml paml4.9j/examples/TipDate.FluH1/H1.NodeNumbers.tre paml4.9j/examples/TipDate.FluH1/H1.nexus paml4.9j/examples/TipDate.FluH1/H1.tre paml4.9j/examples/TipDate.FluH1/H1.txt paml4.9j/examples/TipDate.FluH1/baseml.ctl paml4.9j/examples/TipDate.FluH1/commands.txt paml4.9j/examples/TipDate.FluH1/in.BV.HKYG5 paml4.9j/examples/TipDate.FluH1/mcmctreeClock1.ctl paml4.9j/examples/TipDate.FluH1/mcmctreeClock2.ctl paml4.9j/examples/TipDate.FluH1/mcmctreeClock3.ctl paml4.9j/examples/TipDate.HIV2/ paml4.9j/examples/TipDate.HIV2/FigTree.tre paml4.9j/examples/TipDate.HIV2/HIV2ge.tre paml4.9j/examples/TipDate.HIV2/HIV2ge.txt paml4.9j/examples/TipDate.HIV2/README.txt paml4.9j/examples/TipDate.HIV2/baseml.ctl paml4.9j/examples/TipDate.HIV2/in.BV.HKYG5 paml4.9j/examples/TipDate.HIV2/mcmctree.ExactlnL.ctl paml4.9j/examples/TipDate.HIV2/mcmctree.ctl paml4.9j/examples/YN00abglobin.result paml4.9j/examples/abglobin.aa paml4.9j/examples/abglobin.nuc paml4.9j/examples/abglobin.trees paml4.9j/examples/dNdSGene1.nuc paml4.9j/examples/horai.nuc paml4.9j/examples/horai.trees paml4.9j/examples/lysin/ paml4.9j/examples/lysin/README.txt paml4.9j/examples/lysin/RasMol.txt paml4.9j/examples/lysin/SiteNumbering.txt paml4.9j/examples/lysin/codeml.ctl paml4.9j/examples/lysin/codemlYangSwanson2002.ctl paml4.9j/examples/lysin/lysin.nuc paml4.9j/examples/lysin/lysin.trees paml4.9j/examples/lysin/lysinYangSwanson2002.nuc paml4.9j/examples/lysozyme/ paml4.9j/examples/lysozyme/README.txt paml4.9j/examples/lysozyme/codeml.ctl paml4.9j/examples/lysozyme/lysozymeLarge.ctl paml4.9j/examples/lysozyme/lysozymeLarge.nuc paml4.9j/examples/lysozyme/lysozymeLarge.trees paml4.9j/examples/lysozyme/lysozymeSmall.ctl paml4.9j/examples/lysozyme/lysozymeSmall.nuc paml4.9j/examples/lysozyme/lysozymeSmall.trees paml4.9j/examples/lysozyme/lysozymeSmall.txt paml4.9j/examples/mtCDNA/ paml4.9j/examples/mtCDNA/AAcodon.result.txt paml4.9j/examples/mtCDNA/README.txt paml4.9j/examples/mtCDNA/codeml.AAcodon.ctl paml4.9j/examples/mtCDNA/codeml.ctl paml4.9j/examples/mtCDNA/miyata.dat paml4.9j/examples/mtCDNA/mtCDNAmam.nuc paml4.9j/examples/mtCDNA/mtCDNAmam.trees paml4.9j/examples/mtCDNA/mtCDNApri.aa paml4.9j/examples/mtCDNA/mtCDNApri.nuc paml4.9j/examples/mtCDNA/mtCDNApri.trees paml4.9j/examples/mtCDNAape/ paml4.9j/examples/mtCDNAape/2s.trees paml4.9j/examples/mtCDNAape/OmegaAA.dat paml4.9j/examples/mtCDNAape/README.txt paml4.9j/examples/mtCDNAape/codeml.HC.ctl paml4.9j/examples/mtCDNAape/codeml.ctl paml4.9j/examples/mtCDNAape/mtCDNA.HC.txt paml4.9j/examples/mtCDNAape/mtCDNAape.trees paml4.9j/examples/mtCDNAape/mtCDNAape.txt paml4.9j/examples/mtprim9.nuc paml4.9j/mcmctree.ctl paml4.9j/pamp.ctl paml4.9j/paupblock paml4.9j/paupend paml4.9j/paupstart paml4.9j/src/ paml4.9j/src/BFdriver.c paml4.9j/src/Makefile paml4.9j/src/Makefile.MSC paml4.9j/src/README.txt paml4.9j/src/TreeTimeJeff.c paml4.9j/src/baseml.c paml4.9j/src/basemlg.c paml4.9j/src/chi2.c paml4.9j/src/codeml.c paml4.9j/src/ds.c paml4.9j/src/evolver.c paml4.9j/src/mcmctree.c paml4.9j/src/paml.h paml4.9j/src/pamp.c paml4.9j/src/tools.c paml4.9j/src/treespace.c paml4.9j/src/treesub.c paml4.9j/src/yn00.c paml4.9j/stewart.aa paml4.9j/stewart.trees paml4.9j/yn00.ctl cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o baseml baseml.c tools.c -lm In file included from baseml.c:131: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from baseml.c:11: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o codeml codeml.c tools.c -lm In file included from codeml.c:238: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from codeml.c:17: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o basemlg basemlg.c tools.c -lm In file included from basemlg.c:80: treesub.c: In function ‘ReadSeq’: treesub.c:858:31: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 858 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ In file included from basemlg.c:80: treesub.c:866:28: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 866 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ In file included from basemlg.c:80: treesub.c: In function ‘printPatterns’: treesub.c:1093:25: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 1093 | printsma(fout, com.spname, com.z, com.ns, com.npatt, com.npatt, gap, com.seqtype, 1, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ In file included from basemlg.c:80: treesub.c: In function ‘AllPatterns’: treesub.c:1361:25: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 1361 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o mcmctree mcmctree.c tools.c -lm In file included from mcmctree.c:210: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from mcmctree.c:22: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -lm In file included from mcmctree.c:210: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from mcmctree.c:22: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o pamp pamp.c tools.c -lm In file included from pamp.c:66: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from pamp.c:8: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o evolver evolver.c tools.c -lm cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o yn00 yn00.c tools.c -lm In file included from yn00.c:70: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from yn00.c:13: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ cc -O2 -march=i586 -mtune=i686 -fcommon -O3 -o chi2 chi2.c -lm Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/paml/paml-4.9j-i586-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/baseml usr/bin/basemlg usr/bin/chi2 usr/bin/codeml usr/bin/evolver usr/bin/mcmctree usr/bin/pamp usr/bin/yn00 usr/doc/ usr/doc/paml-4.9j/ usr/doc/paml-4.9j/GeneticCode.txt usr/doc/paml-4.9j/LICENSE usr/doc/paml-4.9j/MCMCtree.Tutorial.pdf usr/doc/paml-4.9j/MCMCtree.Tutorials.pdf usr/doc/paml-4.9j/README-codon.txt usr/doc/paml-4.9j/README-compiling.txt usr/doc/paml-4.9j/README.txt usr/doc/paml-4.9j/eigenQREV.pdf usr/doc/paml-4.9j/multiruns.txt usr/doc/paml-4.9j/paml.SlackBuild usr/doc/paml-4.9j/pamlDOC.pdf usr/doc/paml-4.9j/pamlFAQs.pdf usr/doc/paml-4.9j/pamlHistory.txt usr/libexec/ usr/libexec/paml/ usr/libexec/paml/PositiveSitesBEB usr/libexec/paml/PositiveSitesBS usr/libexec/paml/PositiveSitesNEB usr/libexec/paml/evolverNSbranches usr/libexec/paml/evolverNSbranchsites usr/libexec/paml/evolverNSsites usr/libexec/paml/multiruns usr/share/ usr/share/paml/ usr/share/paml/aa/ usr/share/paml/aa/stewart.aa usr/share/paml/codon/ usr/share/paml/codon/MCcodonNSbranches.dat usr/share/paml/codon/MCcodonNSbranchsites.dat usr/share/paml/codon/MCcodonNSclade.dat usr/share/paml/codon/MCcodonNSsites.dat usr/share/paml/codon/codeml.ctl usr/share/paml/ctl/ usr/share/paml/ctl/aaml.ctl usr/share/paml/ctl/baseml.ctl usr/share/paml/ctl/codeml.ctl usr/share/paml/ctl/codonml.ctl usr/share/paml/ctl/mcmctree.ctl usr/share/paml/ctl/pamp.ctl usr/share/paml/ctl/yn00.ctl usr/share/paml/dat/ usr/share/paml/dat/MCaa.dat usr/share/paml/dat/MCbase.dat usr/share/paml/dat/MCbaseRandomTree.dat usr/share/paml/dat/MCcodon.dat usr/share/paml/dat/MtZoa.dat usr/share/paml/dat/cpREV10.dat usr/share/paml/dat/cpREV64.dat usr/share/paml/dat/dayhoff-dcmut.dat usr/share/paml/dat/dayhoff.dat usr/share/paml/dat/g1974a.dat usr/share/paml/dat/g1974c.dat usr/share/paml/dat/g1974p.dat usr/share/paml/dat/g1974v.dat usr/share/paml/dat/grantham.dat usr/share/paml/dat/jones-dcmut.dat usr/share/paml/dat/jones.dat usr/share/paml/dat/lg.dat usr/share/paml/dat/miyata.dat usr/share/paml/dat/mtArt.dat usr/share/paml/dat/mtREV24.dat usr/share/paml/dat/mtmam.dat usr/share/paml/dat/wag.dat usr/share/paml/examples/ usr/share/paml/examples/9s.trees usr/share/paml/examples/CladeModelCD/ usr/share/paml/examples/CladeModelCD/ECP_EDN_15.nuc usr/share/paml/examples/CladeModelCD/PAMLCladeModelCDnotes.pdf usr/share/paml/examples/CladeModelCD/codeml.CladeC.ctl usr/share/paml/examples/CladeModelCD/codeml.CladeD.ctl usr/share/paml/examples/CladeModelCD/tree.txt usr/share/paml/examples/DatingSoftBound/ usr/share/paml/examples/DatingSoftBound/BF.Clock23.xlsx usr/share/paml/examples/DatingSoftBound/BFdriverDOC.pdf usr/share/paml/examples/DatingSoftBound/FixedDsClock23.txt usr/share/paml/examples/DatingSoftBound/README.BayesFactor.txt usr/share/paml/examples/DatingSoftBound/README.txt usr/share/paml/examples/DatingSoftBound/bf1/ usr/share/paml/examples/DatingSoftBound/bf1/mcmctree.ctl usr/share/paml/examples/DatingSoftBound/bf2/ usr/share/paml/examples/DatingSoftBound/bf2/mcmctree.ctl usr/share/paml/examples/DatingSoftBound/mcmctree.Infinitesites.ctl usr/share/paml/examples/DatingSoftBound/mcmctree.ctl usr/share/paml/examples/DatingSoftBound/mtCDNApri.trees usr/share/paml/examples/DatingSoftBound/mtCDNApri123.txt usr/share/paml/examples/HIVNSsites/ usr/share/paml/examples/HIVNSsites/HIVenvSweden.trees usr/share/paml/examples/HIVNSsites/HIVenvSweden.txt usr/share/paml/examples/HIVNSsites/HIVenvSweden4s.trees usr/share/paml/examples/HIVNSsites/HIVenvSweden4s.txt usr/share/paml/examples/HIVNSsites/README.txt usr/share/paml/examples/HIVNSsites/codeml.ctl usr/share/paml/examples/MHC.Swanson2002MBE/ usr/share/paml/examples/MHC.Swanson2002MBE/README.txt usr/share/paml/examples/MHC.Swanson2002MBE/bigmhc.phy usr/share/paml/examples/MHC.Swanson2002MBE/bigmhc.trees usr/share/paml/examples/MHC.Swanson2002MBE/codeml.ctl usr/share/paml/examples/MouseLemurs/ usr/share/paml/examples/MouseLemurs/MouseLemurs.aa usr/share/paml/examples/MouseLemurs/MouseLemurs.nuc usr/share/paml/examples/MouseLemurs/MouseLemurs.trees usr/share/paml/examples/MouseLemurs/MouseLemurs123.nuc usr/share/paml/examples/MouseLemurs/README.txt usr/share/paml/examples/MouseLemurs/README2.txt usr/share/paml/examples/MouseLemurs/aaml.ctl usr/share/paml/examples/MouseLemurs/aaml2.ctl usr/share/paml/examples/MouseLemurs/baseml.ctl usr/share/paml/examples/MouseLemurs/baseml2.ctl usr/share/paml/examples/MouseLemurs/codeml.ctl usr/share/paml/examples/MouseLemurs/codonml.ctl usr/share/paml/examples/MouseLemurs/codonml2.ctl usr/share/paml/examples/MouseLemurs/mtmam.dat usr/share/paml/examples/README.txt usr/share/paml/examples/TipDate.FluH1/ usr/share/paml/examples/TipDate.FluH1/H1.Beast.Nulldata.xml usr/share/paml/examples/TipDate.FluH1/H1.Beast.xml usr/share/paml/examples/TipDate.FluH1/H1.NodeNumbers.tre usr/share/paml/examples/TipDate.FluH1/H1.nexus usr/share/paml/examples/TipDate.FluH1/H1.tre usr/share/paml/examples/TipDate.FluH1/H1.txt usr/share/paml/examples/TipDate.FluH1/baseml.ctl usr/share/paml/examples/TipDate.FluH1/commands.txt usr/share/paml/examples/TipDate.FluH1/in.BV.HKYG5 usr/share/paml/examples/TipDate.FluH1/mcmctreeClock1.ctl usr/share/paml/examples/TipDate.FluH1/mcmctreeClock2.ctl usr/share/paml/examples/TipDate.FluH1/mcmctreeClock3.ctl usr/share/paml/examples/TipDate.HIV2/ usr/share/paml/examples/TipDate.HIV2/FigTree.tre usr/share/paml/examples/TipDate.HIV2/HIV2ge.tre usr/share/paml/examples/TipDate.HIV2/HIV2ge.txt usr/share/paml/examples/TipDate.HIV2/README.txt usr/share/paml/examples/TipDate.HIV2/baseml.ctl usr/share/paml/examples/TipDate.HIV2/in.BV.HKYG5 usr/share/paml/examples/TipDate.HIV2/mcmctree.ExactlnL.ctl usr/share/paml/examples/TipDate.HIV2/mcmctree.ctl usr/share/paml/examples/YN00abglobin.result usr/share/paml/examples/abglobin.aa usr/share/paml/examples/abglobin.nuc usr/share/paml/examples/abglobin.trees usr/share/paml/examples/dNdSGene1.nuc usr/share/paml/examples/horai.nuc usr/share/paml/examples/horai.trees usr/share/paml/examples/lysin/ usr/share/paml/examples/lysin/README.txt usr/share/paml/examples/lysin/RasMol.txt usr/share/paml/examples/lysin/SiteNumbering.txt usr/share/paml/examples/lysin/codeml.ctl usr/share/paml/examples/lysin/codemlYangSwanson2002.ctl usr/share/paml/examples/lysin/lysin.nuc usr/share/paml/examples/lysin/lysin.trees usr/share/paml/examples/lysin/lysinYangSwanson2002.nuc usr/share/paml/examples/lysozyme/ usr/share/paml/examples/lysozyme/README.txt usr/share/paml/examples/lysozyme/codeml.ctl usr/share/paml/examples/lysozyme/lysozymeLarge.ctl usr/share/paml/examples/lysozyme/lysozymeLarge.nuc usr/share/paml/examples/lysozyme/lysozymeLarge.trees usr/share/paml/examples/lysozyme/lysozymeSmall.ctl usr/share/paml/examples/lysozyme/lysozymeSmall.nuc usr/share/paml/examples/lysozyme/lysozymeSmall.trees usr/share/paml/examples/lysozyme/lysozymeSmall.txt usr/share/paml/examples/mtCDNA/ usr/share/paml/examples/mtCDNA/AAcodon.result.txt usr/share/paml/examples/mtCDNA/README.txt usr/share/paml/examples/mtCDNA/codeml.AAcodon.ctl usr/share/paml/examples/mtCDNA/codeml.ctl usr/share/paml/examples/mtCDNA/miyata.dat usr/share/paml/examples/mtCDNA/mtCDNAmam.nuc usr/share/paml/examples/mtCDNA/mtCDNAmam.trees usr/share/paml/examples/mtCDNA/mtCDNApri.aa usr/share/paml/examples/mtCDNA/mtCDNApri.nuc usr/share/paml/examples/mtCDNA/mtCDNApri.trees usr/share/paml/examples/mtCDNAape/ usr/share/paml/examples/mtCDNAape/2s.trees usr/share/paml/examples/mtCDNAape/OmegaAA.dat usr/share/paml/examples/mtCDNAape/README.txt usr/share/paml/examples/mtCDNAape/codeml.HC.ctl usr/share/paml/examples/mtCDNAape/codeml.ctl usr/share/paml/examples/mtCDNAape/mtCDNA.HC.txt usr/share/paml/examples/mtCDNAape/mtCDNAape.trees usr/share/paml/examples/mtCDNAape/mtCDNAape.txt usr/share/paml/examples/mtprim9.nuc usr/share/paml/nuc/ usr/share/paml/nuc/brown.nuc usr/share/paml/paup/ usr/share/paml/paup/paupblock usr/share/paml/paup/paupend usr/share/paml/paup/paupstart usr/share/paml/trees/ usr/share/paml/trees/3s.trees usr/share/paml/trees/4s.trees usr/share/paml/trees/5s.trees usr/share/paml/trees/6s.trees usr/share/paml/trees/brown.rooted.trees usr/share/paml/trees/brown.trees usr/share/paml/trees/stewart.trees Slackware package /usr/src/slapt-src/academic/paml/paml-4.9j-i586-1salix15.0.txz created. Installing package paml-4.9j-i586-1salix15.0... | paml (PAML: Phylogenetic Analysis by Maximum Likelihood) | | PAML is a package of programs for phylogenetic analyses of DNA or | protein sequences using maximum likelihood. PAML is not good for | tree making. It may be used to estimate parameters and test | hypotheses to study the evolutionary process, when you have | reconstructed trees using other programs such as PAUP*, PHYLIP, | MOLPHY, PhyML, RaxML, etc. | | Home: http://abacus.gene.ucl.ac.uk/software/paml.html | | |