ips-package | Interfaces to Phylogenetic Software |
aliscore | Masking of Sequence Alignments with ALISCORE |
code.simple.gaps | Simple Gap/Indel Coding |
collapseUnsupportedEdges | Collapse Unsupported Edges |
delete.gaps | Remove Gap/Indel Positions from Alignment |
deleteEmptyCells | Delete Spurious Rows and Columns from DNA Alignments |
deleteGaps | Remove Gap/Indel Positions from Alignment |
descendants | Descendants of an Internal Node in a Phylogeny |
fillEndsWithN | Trim Alignment Ends |
fixNodes | Standard Node Numbering in Phylo Objects |
gblocks | Masking of Sequence Alignments with GBLOCKS |
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 | DNA Sequence Alignment with MAFFT |
mrbayes | Bayesian MCMC Tree Search with MrBayes |
mrbayes.mixed | Bayesian MCMC Tree Search with MrBayes |
multistate | MULTISTATE |
multistateMCMC | MULTISTATE |
multistateML | MULTISTATE |
noi | Identification of MRCAs for Clades |
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 |
read.beast | Read Bayesian Trees |
read.beast.table | Extract node data from BEAST chronogram |
read.fas | Read DNA Sequences |
read.mrbayes | Read Bayesian Trees |
read.nex | Read DNA Sequences |
read.phy | Read DNA Sequences |
read.starbeast | Read Bayesian Trees |
sister | Identification of Sister Nodes and Clades |
tipHeights | Tip Heights in a Phylogenetic Tree |
traitRate | Trait-Dependent Shifts in Molecular Rate |
trimEnds | Trim Alignment Ends |
write.fas | Write DNA Sequences to File |
write.nex | Write DNA Sequences to File |
write.partitioned.nex | Write partitioned and commented NEXUS files |
write.phy | Write DNA Sequences to File |