Man pages for andrew-hipp/morton
Tools for manipulation of phylogenetic, genetic, and other biodiversity data
| add.data.to.tips | Adds data to the tip labels of a tree using a standard... |
| color.tips.by.element | Color the tip labels of a tree according to elements of the... |
| fas2bin | Convert a File in FASTA Format to Binary |
| gene.matrix.stats | 'Summary' method for gene.matrix. |
| label.elements | Extract Information from Tip Labels of a Phylogenetic Tree |
| make.binary | Convert a Character Matrix to a Binary Character Matrix |
| make.gene.matrix | Linkage of Specimens to Sequences for Multiple Loci |
| make.shared.gene.matrix | Count Shared Specimens Between Loci |
| make.unique.vouchers | Assign Specimen Vouchers to Gene Sequences |
| match.nodes | Match and Plot Nodes of Multiple Trees |
| monophyletic.spp | Summary of Species Coverage and Monophyly |
| morton-package | Tools for manipulation of phylogenetic, genetic, and other... |
| morton-undocumented-beast | undocumented morton functions - BEAST dating |
| morton-undocumented-haversine | undocumented morton functions - haversine |
| morton-undocumented-mantel | undocumented morton functions - mantel |
| morton-undocumented-neiD | undocumented morton functions - neiD |
| morton-undocumented-other | undocumented morton functions - other |
| morton-undocumented-rate.change | undocumented morton functions - rate.change |
| orphan.individuals | Identify Vouchers Lacking Sequences |
| orphan.loci | Identify Gene Loci Lacking Sequences. |
| parse.INSDSeq | Parse Raw Gene Database Data from XML File |
| parse.specimen | Parse the Specimen Field From a Parsed XML File |
| plot.geneMat | Plot Gene Coverage of All Individuals |
| refine.fasta | Clean Up FASTA Files to User Specification |
| section.coloring | Color Tree Tips by Section |
| summarize.gene.coverage | Plot Individuals Sequenced Per Gene |
| summary.by.elements | Calculate Taxonomic Disparity For All Taxa |
| tidyName | Clean Up Strings |
| tips.expected | Calculate Expected Tips in a Clade |
