News

catGenes 1.0.0

Initial Release

The first official release of the catGenes R package, designed to support reproducible phylogenetic and phylogenomic workflows in R, from sequence retrieval and alignment preparation to dataset concatenation, model selection, Bayesian inference, and tree visualization.

Core functionality

mineSeq(): Retrieve DNA sequences from GenBank using accession numbers.
mineTaxa(): Retrieve DNA sequences from GenBank using taxonomic query terms.
minePlastome(): Mine targeted loci from plastid genomes available in GenBank.
mineMitochondrion(): Mine targeted loci from mitochondrial genomes available in GenBank.
combineFASTA(): Combine multiple FASTA files into a single sequence file.
alignSeqs(): Perform automated multiple sequence alignment using supported algorithms.
convertAlign(): Convert alignments among FASTA, NEXUS, and PHYLIP formats.

Multilocus dataset assembly

catfullGenes(): Compare and prepare multiple alignments for concatenation when taxa are represented by a single sequence per locus.
catmultGenes(): Compare and prepare multiple alignments for concatenation when one or more taxa are represented by multiple accessions.
dropSeq(): Remove redundant or less informative duplicated accessions from concatenated datasets.
writeNexus(): Export concatenated datasets in NEXUS format, optionally including partition definitions and a preliminary MrBayes block.
writePhylip(): Export concatenated datasets in PHYLIP format and generate a partition file for downstream analyses.

Phylogenetic analysis and visualization

evomodelTest(): Perform evolutionary model selection and generate MrBayes-ready command blocks.
mrbayesRun(): Run MrBayes directly from R using an existing NEXUS file.
plotPhylo(): Plot and edit phylogenetic trees using ggtree.

Package infrastructure

MIT license.
Continuous integration via GitHub Actions.
Function reference and articles hosted at the package website.
README and website materials updated to reflect the broader scope of the package beyond alignment concatenation.

Website

Package documentation is available at:
https://dboslab.github.io/catGenes-website/

Feedback

Please report bugs, issues, or suggestions at:
https://github.com/DBOSlab/catGenes/issues

--- title: "News" format: html: toc: true toc-depth: 3 --- <style> body { background-image: url('/figures/reflora_bg.png'); background-repeat: repeat-y; background-size: cover; background-attachment: fixed; background-position: top center; position: relative; z-index: 0; } .background-overlay { position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: rgba(255, 255, 255, 0.8); /* white with 80% opacity */ z-index: -1; } </style> # catGenes 1.0.0 ## Initial Release The first official release of the `catGenes` R package, designed to support reproducible phylogenetic and phylogenomic workflows in R, from sequence retrieval and alignment preparation to dataset concatenation, model selection, Bayesian inference, and tree visualization. ### Core functionality - `mineSeq()`: Retrieve DNA sequences from GenBank using accession numbers. - `mineTaxa()`: Retrieve DNA sequences from GenBank using taxonomic query terms. - `minePlastome()`: Mine targeted loci from plastid genomes available in GenBank. - `mineMitochondrion()`: Mine targeted loci from mitochondrial genomes available in GenBank. - `combineFASTA()`: Combine multiple FASTA files into a single sequence file. - `alignSeqs()`: Perform automated multiple sequence alignment using supported algorithms. - `convertAlign()`: Convert alignments among `FASTA`, `NEXUS`, and `PHYLIP` formats. ### Multilocus dataset assembly - `catfullGenes()`: Compare and prepare multiple alignments for concatenation when taxa are represented by a single sequence per locus. - `catmultGenes()`: Compare and prepare multiple alignments for concatenation when one or more taxa are represented by multiple accessions. - `dropSeq()`: Remove redundant or less informative duplicated accessions from concatenated datasets. - `writeNexus()`: Export concatenated datasets in `NEXUS` format, optionally including partition definitions and a preliminary `MrBayes` block. - `writePhylip()`: Export concatenated datasets in `PHYLIP` format and generate a partition file for downstream analyses. ### Phylogenetic analysis and visualization - `evomodelTest()`: Perform evolutionary model selection and generate `MrBayes`-ready command blocks. - `mrbayesRun()`: Run `MrBayes` directly from R using an existing `NEXUS` file. - `plotPhylo()`: Plot and edit phylogenetic trees using `ggtree`. ### Package infrastructure - MIT license. - Continuous integration via GitHub Actions. - Function reference and articles hosted at the package website. - README and website materials updated to reflect the broader scope of the package beyond alignment concatenation. ### Website Package documentation is available at: <https://dboslab.github.io/catGenes-website/> ### Feedback Please report bugs, issues, or suggestions at: <https://github.com/DBOSlab/catGenes/issues>