Man pages for fmichonneau/phyloch
Tools for phylogenetics and taxonomy

add.geoscaleGeological Time Scale for Phylogenies
add.timeframeHigh-lighting ages in chronograms
add.trendlinePlotting Trendlines on a Phylogeny
aliscoreCleaning of Sequence Alignments
append2tipsAppend Symbols or Text to Tip Labels
axisChronoAxis for time-calibrated phylogenies
axisGeoGeological Time Axis for Time-Calibrated Phylogenies
c.alignmentConcatenation of DNA Sequences
clade.barsPlot Bars beside Clades in a Phylogeny
code.simple.gapsSimple Gap/Indel Coding
compare.phyloCompare PHYLO Objects Graphically
continousMLML Estimation of Continous Traits
delete.empty.cellsDelete empty rows and columns from a DNA sequence alignment
delete.gapsRemove Indel Positions from an Alignment
descendantsDescendants of an Internal Node in a Phylogeny
draw.boxesPlot Boxes around Clades in a Phylogeny
drop.tip2Remove Tips from a Phylogenetic Tree
edge.colorColors for Tips and Edges in Phylogenies
extract.clade2Extract Clades from a Phylogentic Tree
fillEndsWithNFill alignment ends with N
fixNodesStandard Node Numbering in Phylo Objects
gblocksCleaning of Sequence Alignments
gradstein04Stratigraphic Chart 2004
homogen.base.freqHomogeneity of base frequencies
hordeumPhylogeny of Wild Barley (Hordeum)
HPDbarsPlot HPD Intervals on Time-calibrated Phylogenies
ident.seqIdentify or delete identical DNA sequences
is.consecutiveIs Node Numbering Consecutive?
mafftDNA Sequence Alignment with MAFFT
mrbayesBayesian MCMC Tree Search with MrBayes
nodeInfoGraphical Annotation of Internal Nodes
node.supportVisualizing Node Support on Phylogenetic Trees
node.transTranslate Internal Node Indices between Trees
noiIdentification of MRCAs for Taxon Sets
phylo3D3D Geophylogenies for GIS Applications
phyloch-internalInternal Phyloch Functions
phyloch-packagePhylogenetic Data Analysis And Display
pisNumber of parsimony-informative sites
plotNetworkPlot Haplotype/Genotype Networks
plot.phylo.uponHelper function
raxmlMaximium Likelihood Tree Search
rbeautiXML Input Files for BEAST
read.beastRead Bayesian Trees
read.beast.tableExtract node data from BEAST chronogram
read.fasRead DNA Sequences
rotate2Swapping Sister Clades
shiftNodeAgeModify Node Ages in Ultramtric Trees
sisterIdentification of Sister Nodes and Clades
strat2012Stratigraphic Chart 2012
string.dimDimensions of Rotated Strings
taxo.fontsFont Types for Tip Labels
viperaPhylogenetic Trees of True Vipers
write.fasWrite DNA Sequences to File
write.partitioned.nexWrite partitioned and commented NEXUS files
fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.