ips-internal
(Package: ips) :
Internal IPS Functions
Internal ips functions.
● Data Source:
CranContrib
● Keywords: internal
● Alias: extractBEASTstats, extractMRBAYESstats, phylo2mafft, rbeauti.taxonset, read.xml, terminal.clades, traitRateOutput, traitRateParams, unresolve.clade
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gblocks
(Package: ips) :
Masking of Sequence Alignments with GBLOCKS
This function provides a wrapper to Gblocks, a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. Gblocks selects conserved blocks from a multiple alignment according to a set of features of the alignment positions.
● Data Source:
CranContrib
● Keywords:
● Alias: gblocks
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deleteGaps
(Package: ips) :
Remove Gap/Indel Positions from Alignment
This function removes indel positions (or gaps) from a DNA sequence alignment. For faster execution, deleteGaps handles sequences in ape's bit-level coding scheme.
● Data Source:
CranContrib
● Keywords:
● Alias: delete.gaps, deleteGaps
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read.fas
(Package: ips) :
Read DNA Sequences
This functions parse DNA sequences in FASTA, PHILIP, and NEXUS formatted files.
● Data Source:
CranContrib
● Keywords:
● Alias: read.fas, read.nex, read.phy
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ips-package
(Package: ips) :
Interfaces to Phylogenetic Software
This package presents a set of functions that were formerly included in the phyloch package and which wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.
● Data Source:
CranContrib
● Keywords: package
● Alias: ips, ips-package
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noi
(Package: ips) :
Identification of MRCAs for Clades
This function identifies the most recent common ancestor (MRCA) nodes for one or more sets of taxa/tips.
● Data Source:
CranContrib
● Keywords:
● Alias: noi
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traitRate
(Package: ips) :
Trait-Dependent Shifts in Molecular Rate
Detection of trait-dependent shifts in the rate of molecular evolution with traitRate (Mayrose & Otto, 2011).
● Data Source:
CranContrib
● Keywords:
● Alias: traitRate
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aliscore
(Package: ips) :
Masking of Sequence Alignments with ALISCORE
This function provides a wrapper to Aliscore, which can be used remove problematic regions of a sequence alignment.
● Data Source:
CranContrib
● Keywords:
● Alias: aliscore
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For each tip (leave, terminal node) in the phylogenetic tree the edge lengths (branch lengths) from root to tip, be it units of time or divergence, is summed up.
● Data Source:
CranContrib
● Keywords:
● Alias: tipHeights
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sister
(Package: ips) :
Identification of Sister Nodes and Clades
For any given internal node in a phylogeny, this function returns the sister clade
● Data Source:
CranContrib
● Keywords:
● Alias: sister
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providing 
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