Interfaces to Phylogenetic Software in R
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Documentation for package ‘ips’ version 0.0.12
Help Pages
| ips-package | Interfaces to Phylogenetic Software |
| aliscore | Masking of Sequence Alignments with ALISCORE |
| blastn | Nucleotide-Nucleotide BLAST |
| code.simple.gaps | Simple Gap/Indel Coding |
| collapseUnsupportedEdges | Collapse Unsupported Edges/Branches in a Phylogeny |
| combMyTree | Graft Polytomies on Tips of Phylogeny |
| del.miss | Delete Missing Data from DNA Sequences |
| deleteEmptyCells | Identify/Delete Spurious Rows and Columns from DNA Alignments |
| deleteGaps | Remove Gap Positions From DNA Sequences |
| descendants | Descendants of an Internal Node in a Phylogeny |
| DNAbin2index | Conversion of DNAbin to Index |
| EmptyCells | Identify/Delete Spurious Rows and Columns from DNA Alignments |
| eoi | Identification of Stem-Lineage-Edges and MRCAs |
| fixNodes | Standard Node Numbering in Phylo Objects |
| forceEqualTipHeights | Equal Tip Heights |
| gblocks | Masking of Sequence Alignments with GBLOCKS |
| identifyEmptyCells | Identify/Delete Spurious Rows and Columns from DNA Alignments |
| index2DNAbin | Conversion of Index to DNAbin |
| ips | Interfaces to Phylogenetic Software |
| ips.16S | Bark Beetle 16S Sequences |
| ips.28S | Bark Beetle 28S Sequences |
| ips.cox1 | Bark Beetle COX1 Sequences |
| ips.tree | Ips Phylogeny |
| mafft | Sequence Alignment with MAFFT |
| mafft.merge | Profile Alignment with MAFFT |
| mrbayes | Bayesian MCMC Tree Search with MrBayes |
| mrbayes.lset | Model Settings for MrBayes |
| mrbayes.mcmc | MCMC Settings for MrBayes |
| mrbayes.prset | Set Priors for MrBayes |
| multistate | MULTISTATE |
| multistateMCMC | MULTISTATE |
| multistateML | MULTISTATE |
| neighboringPairs | Neighboring Nodes in a Minimum Spanning Tree |
| noi | Identification of Stem-Lineage-Edges and MRCAs |
| ntip | Numbers of Tips of (Sub)trees |
| oi | Identification of Stem-Lineage-Edges and MRCAs |
| partitionfinder | PartitionFinder |
| pathd8 | PATHd8 |
| phylo2mafft | Convert Trees for MAFFT |
| phylo2mst | Conversion from PHYLO to MST Object |
| pis | Number of Potentially-Informative Sites |
| prank | PRANK |
| raxml | Maximum Likelihood Tree Estimation with RAxML |
| raxml.partitions | Partition scheme for RAxML |
| rbeauti | XML Input Files for BEAST |
| rc | Reverse-Complement of DNA sequences |
| read | Reading Sequence Files |
| read.beast | Read Bayesian Trees |
| read.beast.table | Extract node data from BEAST chronogram |
| read.fas | Reading Sequence Files |
| read.mrbayes | Read Bayesian Trees |
| read.nex | Reading Sequence Files |
| read.phy | Reading Sequence Files |
| read.starbeast | Read Bayesian Trees |
| sister | Identification of Sister Nodes and Clades |
| splitIntoClades | Find Monophyletic Subsets in Species Lists |
| terminalSisters | Find Pairs of Sister Species |
| tipHeights | Tip Heights in a Phylogenetic Tree |
| traitRate | Trait-Dependent Shifts in Molecular Rate |
| trimEnds | Trim Alignment Ends |
| unlistFirstLevel | Unlist To First Level Only |
| write.fas | Write DNA Sequences to File |
| write.nex | Write DNA Sequences to File |
| write.phy | Write DNA Sequences to File |