Package: ips 0.0.12

Christoph Heibl

ips: Interfaces to Phylogenetic Software in R

Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

Authors:Christoph Heibl [aut, cre], Natalie Cusimano [aut], Franz-Sebastian Krah [aut]

ips_0.0.12.tar.gz
ips_0.0.12.tar.gz(r-4.5-noble)ips_0.0.12.tar.gz(r-4.4-noble)
ips_0.0.12.tgz(r-4.4-emscripten)ips_0.0.12.tgz(r-4.3-emscripten)
ips.pdf |ips.html✨
ips/json (API)
NEWS

# Install 'ips' in R:
install.packages('ips', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.30 score 1 packages 125 scripts 1.1k downloads 10 mentions 62 exports 22 dependencies

Last updated 8 months agofrom:d02460eb10. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-linuxNOTENov 20 2024

Exports:aliscoreassembleDataNodeassembleDistributionNodeassembleInitNodeassembleLoggersassembleStateNodeassembleTreeNodebeastLogblastncode.simple.gapscollapseUnsupportedEdgescombMyTreedel.missdeleteEmptyCellsdeleteGapsdescendantsDNAbin2indexeoifixNodesforceEqualTipHeightsgblocksidentifyEmptyCellsindex2DNAbinmafftmafft.mergemrbayesmrbayes.lsetmrbayes.mcmcmrbayes.prsetmultistateMCMCmultistateMLneighboringPairsnointipoperatorparameterpartitionfinderpathd8phylo2mafftphylo2mstpisprankraxmlraxml.partitionsrbeautircread.beastread.beast.tableread.fasread.nexread.physistersplitIntoCladesterminal.cladesterminalSisterstipHeightstrimEndsunlistFirstLevelunresolve.cladewrite.faswrite.nexwrite.phy

Dependencies:apeclicpp11data.tabledigestfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmephangornpkgconfigplyrquadprogRcpprlangvctrsXML

Readme and manuals

Help Manual

Help pageTopics
Interfaces to Phylogenetic Softwareips-package ips
Masking of Sequence Alignments with ALISCOREaliscore
Nucleotide-Nucleotide BLASTblastn
Simple Gap/Indel Codingcode.simple.gaps
Collapse Unsupported Edges/Branches in a PhylogenycollapseUnsupportedEdges
Graft Polytomies on Tips of PhylogenycombMyTree
Delete Missing Data from DNA Sequencesdel.miss
Remove Gap Positions From DNA SequencesdeleteGaps
Descendants of an Internal Node in a Phylogenydescendants
Conversion of DNAbin to IndexDNAbin2index
Identify/Delete Spurious Rows and Columns from DNA AlignmentsdeleteEmptyCells EmptyCells identifyEmptyCells
Identification of Stem-Lineage-Edges and MRCAseoi noi oi
Standard Node Numbering in Phylo ObjectsfixNodes
Equal Tip HeightsforceEqualTipHeights
Masking of Sequence Alignments with GBLOCKSgblocks
Conversion of Index to DNAbinindex2DNAbin
Bark Beetle 16S Sequencesips.16S
Bark Beetle 28S Sequencesips.28S
Bark Beetle COX1 Sequencesips.cox1
Ips Phylogenyips.tree
Sequence Alignment with MAFFTmafft
Profile Alignment with MAFFTmafft.merge
Bayesian MCMC Tree Search with MrBayesmrbayes
Model Settings for MrBayesmrbayes.lset
MCMC Settings for MrBayesmrbayes.mcmc
Set Priors for MrBayesmrbayes.prset
MULTISTATEmultistate multistateMCMC multistateML
Neighboring Nodes in a Minimum Spanning TreeneighboringPairs
Numbers of Tips of (Sub)treesntip
PartitionFinderpartitionfinder
PATHd8pathd8
Convert Trees for MAFFTphylo2mafft
Conversion from PHYLO to MST Objectphylo2mst
Number of Potentially-Informative Sitespis
PRANKprank
Maximum Likelihood Tree Estimation with RAxMLraxml
Partition scheme for RAxMLraxml.partitions
XML Input Files for BEASTrbeauti
Reverse-Complement of DNA sequencesrc
Reading Sequence Filesread read.fas read.nex read.phy
Read Bayesian Treesread.beast read.mrbayes read.starbeast
Extract node data from BEAST chronogramread.beast.table
Identification of Sister Nodes and Cladessister
Find Monophyletic Subsets in Species ListssplitIntoClades
Find Pairs of Sister SpeciesterminalSisters
Tip Heights in a Phylogenetic TreetipHeights
Trait-Dependent Shifts in Molecular RatetraitRate
Trim Alignment EndstrimEnds
Unlist To First Level OnlyunlistFirstLevel
Write DNA Sequences to Filewrite.fas write.nex write.phy