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| phylotools-package | Phylogenetic tools for ecologists |
| add.mat | Add matrix to current matrix |
| aln2dat | Convert ClustalX alignment data to dataframe |
| appendchar | Paste character according to the longest character. |
| complement | Get the complement sequences |
| dat2phy | Convert dataframe to phylip format |
| del.tree.tip | Randomly Delete tree tip labels |
| dimension | Get the dimension of the matrix defined by "XnYm" labels |
| edgesub | Substitute character for a sequence from both sides. |
| fasta.split | Split the fasta object to fasta objects |
| fmatch | Find the matching index |
| formatXY | Formating XY label |
| framsub | Pattern of substitutions of a dataframe. |
| gini | Gini coefficient of inequality |
| hcreorder | Reorder the height for hclust object |
| imagevect | Image plot of a numeric vector |
| inequality | The inequality of a cutting time |
| meangini | Mean Gini coefficient |
| phy2dat | Convert phylip file to dataframe |
| phylocom.comdist | Calculating phylogenetic comdist using Phylocom |
| phylocom.comstruct | Calculating community phylogenetic structure using Phylocom |
| phylocom.pd | Calculate phylogenetic diversity using Phylocom |
| phylocom.phylosor | Calculating Phylosor similarity |
| phyloshuffle | Tip label shuffling of a phylogenetic tree |
| phylotools | Phylogenetic tools for ecologists |
| plotcut | Cutting the phylogenetic cutting pattern by a given time or times |
| plotscale | Rescaling the individuals occurred in a Forestry Dynamic Plot |
| read.phylip | Read phylip file to memory. |
| rename.fasta | Renaming a fasta object given a reference table |
| resid.tree | The undeleted terminals of a phylogenetic tree |
| reverse | Get the reverse sequence. |
| rh | Generating random time between the oldest node and the latest node |
| rm.col | Delete specified columns for dataframe or matrix |
| RMPD | Ratio of mean phylogenetic distance of two phylogenetic trees |
| seq2fasta | Convert Seq file to fasta format |
| sub.tip.label | Substitute the tip labels of a phylogenetic tree |
| supermat | Build super matrix using PHYLIP files |
| uniquefasta | Deleting duplicated sequences in fasta object |
| write.mat | Save supermatrix |