Frequently Asked Questions

What can I use `catGenes` for?

catGenes is designed to support phylogenetic and phylogenomic workflows in R. It can be used to retrieve DNA sequences from GenBank, mine targeted loci from plastid and mitochondrial genomes, combine and align sequence files, convert among alignment formats, compare and concatenate multilocus datasets, prepare partitioned datasets for downstream analyses, run MrBayes from R, and visualize phylogenetic trees.

How do I install `catGenes`?

Visit the Get Started guide for installation instructions from GitHub.

Is `catGenes` free to use?

Yes. catGenes is open source and distributed under the MIT License.

What kinds of data can `catGenes` handle?

catGenes works with DNA sequence data and alignments commonly used in phylogenetics and phylogenomics. Depending on the function, inputs may include GenBank accession tables, taxonomic search terms, FASTA files, and alignments in FASTA, NEXUS, or PHYLIP format.

Can `catGenes` handle duplicated taxa or multiple accessions?

Yes. One of the main strengths of catGenes is its support for concatenating multilocus datasets in which taxa may be represented by multiple accessions. The function catmultGenes() was developed specifically for this scenario, while catfullGenes() is intended for datasets with a single sequence per taxon per locus.

Can `catGenes` align sequences?

Yes. The function alignSeqs() performs automated multiple sequence alignment using supported algorithms available through the msa package.

Can `catGenes` retrieve sequences from GenBank?

Yes. catGenes includes functions to retrieve sequences from GenBank either by accession numbers (mineSeq()) or by taxonomic query terms (mineTaxa()). It also includes dedicated functions to mine loci from complete plastid and mitochondrial genomes.

Can `catGenes` combine multiple FASTA files before alignment?

Yes. The function combineFASTA() allows you to merge multiple FASTA files into a single file, which can be useful before running automated alignment or downstream sequence processing.

Can `catGenes` export concatenated datasets for phylogenetic analyses?

Yes. catGenes can export concatenated datasets in both NEXUS and PHYLIP formats. It can also generate partition information and preliminary MrBayes command blocks for downstream analyses.

Does `catGenes` run phylogenetic analyses directly?

Partially. catGenes does not implement phylogenetic inference itself, but it helps prepare data for analysis and includes mrbayesRun() to run a local installation of MrBayes directly from R.

Do I need `MrBayes` installed to use `catGenes`?

No. Most functions in catGenes do not require MrBayes. You only need a local MrBayes installation if you want to run Bayesian phylogenetic analyses directly from R using mrbayesRun().

Do I need an internet connection to use `catGenes`?

Only for functions that query online resources. For example, mineSeq(), mineTaxa(), minePlastome(), and mineMitochondrion() require internet access because they connect to GenBank. Functions that work with local files, such as combineFASTA(), alignSeqs(), convertAlign(), catfullGenes(), catmultGenes(), writeNexus(), and writePhylip(), can be used offline once the relevant packages are installed.

Can `catGenes` plot phylogenetic trees?

Yes. The function plotPhylo() provides tools for plotting and editing phylogenetic trees using ggtree, including options for adjusting labels, highlighting clades, and producing publication-ready figures.

Is `catGenes` intended only for plant data?

No. Although many examples and use cases may involve plant datasets, catGenes is designed more broadly for DNA-based phylogenetic and phylogenomic workflows and can be applied to other organismal groups as well.

Who develops `catGenes`?

catGenes is developed by:

Domingos Cardoso (@DBOSlab)
Quezia Cavalcante

The package is maintained within the broader research environment of the Rio de Janeiro Botanical Garden (JBRJ).

Why the name `catGenes`?

The name catGenes originally referred to the package’s core purpose of concatenating multiple gene alignments for combined phylogenetic analyses. As the package evolved, it expanded beyond concatenation to include additional tools for sequence retrieval, alignment processing, model selection, Bayesian analysis support, and tree visualization, while retaining its original name.

Where can I report bugs or request features?

Please submit issues on GitHub: catGenes Issues

Where can I find the source code and documentation?

The source code is available on GitHub: https://github.com/DBOSlab/catGenes

The package website and documentation are available at: https://dboslab.github.io/catGenes-website/

--- title: "Frequently Asked Questions" format: html: toc: true --- <style> body { 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> ### What can I use `catGenes` for? `catGenes` is designed to support phylogenetic and phylogenomic workflows in R. It can be used to retrieve DNA sequences from GenBank, mine targeted loci from plastid and mitochondrial genomes, combine and align sequence files, convert among alignment formats, compare and concatenate multilocus datasets, prepare partitioned datasets for downstream analyses, run `MrBayes` from R, and visualize phylogenetic trees. ### How do I install `catGenes`? Visit the [Get Started guide](/get-started/index.qmd) for installation instructions from GitHub. ### Is `catGenes` free to use? Yes. `catGenes` is open source and distributed under the [MIT License](https://opensource.org/license/mit/). ### What kinds of data can `catGenes` handle? `catGenes` works with DNA sequence data and alignments commonly used in phylogenetics and phylogenomics. Depending on the function, inputs may include GenBank accession tables, taxonomic search terms, `FASTA` files, and alignments in `FASTA`, `NEXUS`, or `PHYLIP` format. ### Can `catGenes` handle duplicated taxa or multiple accessions? Yes. One of the main strengths of `catGenes` is its support for concatenating multilocus datasets in which taxa may be represented by multiple accessions. The function `catmultGenes()` was developed specifically for this scenario, while `catfullGenes()` is intended for datasets with a single sequence per taxon per locus. ### Can `catGenes` align sequences? Yes. The function `alignSeqs()` performs automated multiple sequence alignment using supported algorithms available through the `msa` package. ### Can `catGenes` retrieve sequences from GenBank? Yes. `catGenes` includes functions to retrieve sequences from GenBank either by accession numbers (`mineSeq()`) or by taxonomic query terms (`mineTaxa()`). It also includes dedicated functions to mine loci from complete plastid and mitochondrial genomes. ### Can `catGenes` combine multiple FASTA files before alignment? Yes. The function `combineFASTA()` allows you to merge multiple `FASTA` files into a single file, which can be useful before running automated alignment or downstream sequence processing. ### Can `catGenes` export concatenated datasets for phylogenetic analyses? Yes. `catGenes` can export concatenated datasets in both `NEXUS` and `PHYLIP` formats. It can also generate partition information and preliminary `MrBayes` command blocks for downstream analyses. ### Does `catGenes` run phylogenetic analyses directly? Partially. `catGenes` does not implement phylogenetic inference itself, but it helps prepare data for analysis and includes `mrbayesRun()` to run a local installation of `MrBayes` directly from R. ### Do I need `MrBayes` installed to use `catGenes`? No. Most functions in `catGenes` do not require `MrBayes`. You only need a local `MrBayes` installation if you want to run Bayesian phylogenetic analyses directly from R using `mrbayesRun()`. ### Do I need an internet connection to use `catGenes`? Only for functions that query online resources. For example, `mineSeq()`, `mineTaxa()`, `minePlastome()`, and `mineMitochondrion()` require internet access because they connect to GenBank. Functions that work with local files, such as `combineFASTA()`, `alignSeqs()`, `convertAlign()`, `catfullGenes()`, `catmultGenes()`, `writeNexus()`, and `writePhylip()`, can be used offline once the relevant packages are installed. ### Can `catGenes` plot phylogenetic trees? Yes. The function `plotPhylo()` provides tools for plotting and editing phylogenetic trees using `ggtree`, including options for adjusting labels, highlighting clades, and producing publication-ready figures. ### Is `catGenes` intended only for plant data? No. Although many examples and use cases may involve plant datasets, `catGenes` is designed more broadly for DNA-based phylogenetic and phylogenomic workflows and can be applied to other organismal groups as well. ### Who develops `catGenes`? `catGenes` is developed by: - Domingos Cardoso ([\@DBOSlab](https://github.com/DBOSlab)) - Quezia Cavalcante The package is maintained within the broader research environment of the [Rio de Janeiro Botanical Garden (JBRJ)](https://www.gov.br/jbrj). ### Why the name `catGenes`? The name `catGenes` originally referred to the package’s core purpose of concatenating multiple gene alignments for combined phylogenetic analyses. As the package evolved, it expanded beyond concatenation to include additional tools for sequence retrieval, alignment processing, model selection, Bayesian analysis support, and tree visualization, while retaining its original name. ### Where can I report bugs or request features? Please submit issues on GitHub: [catGenes Issues](https://github.com/DBOSlab/catGenes/issues) ### Where can I find the source code and documentation? The source code is available on GitHub: [https://github.com/DBOSlab/catGenes](https://github.com/DBOSlab/catGenes) The package website and documentation are available at: [https://dboslab.github.io/catGenes-website/](https://dboslab.github.io/catGenes-website/)

What can I use catGenes for?

How do I install catGenes?

Is catGenes free to use?

What kinds of data can catGenes handle?

Can catGenes handle duplicated taxa or multiple accessions?

Can catGenes align sequences?

Can catGenes retrieve sequences from GenBank?

Can catGenes combine multiple FASTA files before alignment?

Can catGenes export concatenated datasets for phylogenetic analyses?

Does catGenes run phylogenetic analyses directly?

Do I need MrBayes installed to use catGenes?

Do I need an internet connection to use catGenes?

Can catGenes plot phylogenetic trees?

Is catGenes intended only for plant data?

Who develops catGenes?

Why the name catGenes?