Table 3.
Functions for importing and exporting data in apex
| Function | Input | Output | Notes |
|---|---|---|---|
| read.multidna | Interleaved, sequential, clustal, fasta files | multidna | Based on read.dna (ape package) |
| read.multiFASTA | Fasta files | multidna | Based on read.FASTA (ape package) |
| read.multiphyDat | Interleaved, fasta | multiphyDat | Based on read.phyDat (phangorn package) can read amino acid sequences |
| multidna2multiphyDat | multidna | multiphyDat | |
| multiphyDat2multidna | multiphyDat | multidna | Only works for DNA sequences |
| multidna2genind | multidna | genind a | Extract either SNPs or haplotypes |
| multiphyDat2genind | multiphyDat | genind a | Extract either SNPs or haplotypes |
a
Base class for genetic markers in the adegenet package.