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
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ips_0.0.12.tgz(r-4.4-any)ips_0.0.12.tgz(r-4.3-any)
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://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/heibl/ips/issues

Datasets:

ips.16S - Bark Beetle 16S Sequences
ips.28S - Bark Beetle 28S Sequences
ips.cox1 - Bark Beetle COX1 Sequences
ips.tree - Ips Phylogeny

On CRAN:

62 exports 10 stars 2.89 score 41 dependencies 2 dependents 10 mentions 116 scripts 1.3k downloads

Last updated 5 months agofrom:2ef779b8ec. Checks:OK: 5 NOTE: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 23 2024
R-4.5-win	NOTE	Aug 23 2024
R-4.5-linux	NOTE	Aug 23 2024
R-4.4-win	OK	Aug 23 2024
R-4.4-mac	OK	Aug 23 2024
R-4.3-win	OK	Aug 23 2024
R-4.3-mac	OK	Aug 23 2024

Exports:aliscore assembleDataNode assembleDistributionNode assembleInitNode assembleLoggers assembleStateNode assembleTreeNode beastLog blastn code.simple.gaps collapseUnsupportedEdges combMyTree del.miss deleteEmptyCells deleteGaps descendants DNAbin2index eoi fixNodes forceEqualTipHeights gblocks identifyEmptyCells index2DNAbin mafft mafft.merge mrbayes mrbayes.lset mrbayes.mcmc mrbayes.prset multistateMCMC multistateML neighboringPairs noi ntip operator parameter partitionfinder pathd8 phylo2mafft phylo2mst pis prank raxml raxml.partitions rbeauti rc read.beast read.beast.table read.fas read.nex read.phy sister splitIntoClades terminal.clades terminalSisters tipHeights trimEnds unlistFirstLevel unresolve.clade write.fas write.nex write.phy

Dependencies:ape cli colorspace cpp11 data.table digest fansi farver fastmatch generics ggplot2 ggseqlogo glue gtable igraph isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme phangorn pillar pkgconfig plyr quadprog R6 RColorBrewer Rcpp rlang scales tibble utf8 vctrs viridisLite withr XML

Citation

Development and contributors

Readme and manuals

Help Manual

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