Files in lliu1871/phybase

Basic functions for phylogenetic analysis

R/alignment.mle.remove.R R/alignment.reference.remove.R R/alignment.site.summary.R R/alignment.summary.R R/alignment.trim.R R/bootstrap.R R/bootstrap.mulgene.R R/control.mpest.R R/del.brlens.R R/del.comments.R R/del.node.R R/dist.dna.R R/dist.internode.R R/dist.species.R R/dist.taxa.R R/file.beast2phylip.R R/file.concatData.R R/file.fasta2phylip.R R/file.nexus2phylip.R R/file.phylip2nexus.R R/file.separateGeneData.R R/is.clock.R R/is.rootedtree.R R/loglike.coal.R R/loglike.triple.R R/node.height.R R/parse.modeltest.R R/parse.phyml.R R/parse.raxml.R R/read.dna.seq.R R/read.tree.nodes.R R/read.tree.string.R R/run.modeltest.R R/run.mpest.R R/run.seqgen.R R/sim.SeqfromSp.R R/sim.coal.mpest.R R/sim.coaltree.R R/sim.coaltree.sp.R R/sim.coaltree.sp.mu.R R/sim.dna.R R/site.pattern.R R/site.summary.R R/species.name.R R/sptree.alleletable.R R/sptree.maxtree.R R/sptree.njst.R R/sptree.star.R R/sptree.steac.R R/test.2sptree.R R/test.equalgenetree.R R/test.hybrid.R R/test.submodel.valid.phyml.R R/test.submodel.valid.raxml.R R/tree.brlens.R R/tree.consensus.R R/tree.distance.R R/tree.name2node.R R/tree.noclock2clock.R R/tree.node2name.R R/tree.partition.R R/tree.plot.R R/tree.probdist.R R/tree.subtree.R R/tree.upgma.R R/write.dna.seq.R R/write.seq.phylip.R R/write.subtree.R R/write.tree.string.R README.md man/alignment.mle.remove.Rd man/alignment.reference.remove.Rd man/alignment.site.summary.Rd man/alignment.summary.Rd man/alignment.trim.Rd man/bootstrap.Rd man/bootstrap.mulgene.Rd man/control.mpest.Rd man/dat.coaltree.Rd man/dat.finch.Rd man/dat.modelcode.Rd man/dat.unrootedtree.Rd man/del.brlens.Rd man/del.comments.Rd man/del.node.Rd man/dist.dna.Rd man/dist.internode.Rd man/dist.species.Rd man/dist.taxa.Rd man/file.beast2phylip.Rd man/file.concatData.Rd man/file.fasta2phylip.Rd man/file.nexus2phylip.Rd man/file.phylip2nexus.Rd man/file.separateGeneData.Rd man/is.clock.Rd man/is.rootedtree.Rd man/loglike.coal.Rd man/loglike.triple.Rd man/node.height.Rd man/parse.modeltest.Rd man/parse.phyml.Rd man/parse.raxml.Rd man/phybase-package.Rd man/read.dna.seq.Rd man/read.tree.nodes.Rd man/read.tree.string.Rd man/run.modeltest.Rd man/run.mpest.Rd man/run.seqgen.Rd man/sim.SeqfromSp.Rd man/sim.coal.mpest.Rd man/sim.coaltree.Rd man/sim.coaltree.sp.Rd man/sim.coaltree.sp.mu.rd man/sim.dna.Rd man/site.pattern.Rd man/site.summary.Rd man/species.name.Rd man/sptree.alleletable.Rd man/sptree.maxtree.Rd man/sptree.njst.Rd man/sptree.star.Rd man/sptree.steac.Rd man/test.2sptree.Rd man/test.equalgenetree.Rd man/test.hybrid.Rd man/test.submodel.valid.phyml.Rd man/test.submodel.valid.raxml.Rd man/tree.brlens.Rd man/tree.consensus.Rd man/tree.distance.Rd man/tree.name2node.Rd man/tree.noclock2clock.Rd man/tree.node2name.Rd man/tree.partition.Rd man/tree.plot.Rd man/tree.probdist.Rd man/tree.subtree.Rd man/tree.upgma.Rd man/write.dna.seq.Rd man/write.seq.phylip.Rd man/write.subtree.Rd man/write.tree.string.Rd phybase2.0-manual.pdf