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 |