Articles

These tutorials provide step-by-step guidance for common catGenes workflows, from sequence retrieval and alignment preparation to multilocus concatenation, phylogenetic analysis support, and tree visualization.

Input preparation

Sequence retrieval and preprocessing

Alignment and concatenation workflows

Export, analysis, and visualization

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These tutorials provide step-by-step guidance for common `catGenes` workflows, from sequence retrieval and alignment preparation to multilocus concatenation, phylogenetic analysis support, and tree visualization.

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### Input preparation
- [Standardizing DNA alignments](/articles/standardizing_alignments.qmd)
- [Loading multiple alignments into R](/articles/loading_alignments.qmd)
- [Working with duplicated taxa and multiple accessions](/articles/duplicated_taxa_and_accessions.qmd)

### Sequence retrieval and preprocessing
- [Retrieve sequences from GenBank with accession numbers](/articles/retrieve_sequences_by_accession.qmd)
- [Retrieve sequences from GenBank with taxonomic queries](/articles/retrieve_sequences_by_taxon.qmd)
- [Mine loci from plastomes and mitochondrial genomes](/articles/mine_organellar_loci.qmd)
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### Alignment and concatenation workflows
- [Combine FASTA files and align sequences](/articles/combine_and_align_sequences.qmd)
- [Convert among FASTA, NEXUS, and PHYLIP](/articles/convert_alignment_formats.qmd)
- [Concatenate multilocus datasets](/articles/concatenate_with_catfullGenes.qmd)
- [Concatenate datasets with duplicated accessions](/articles/concatenate_with_catmultGenes.qmd)
- [Remove redundant accessions](/articles/remove_redundant_accessions.qmd)

### Export, analysis, and visualization
- [Write concatenated datasets](/articles/write_concatenated_datasets.qmd)
- [Model selection and MrBayes preparation](/articles/model_selection_and_mrbayes.qmd)
- [Run MrBayes from R](/articles/run_mrbayes.qmd)
- [Plot and edit phylogenetic trees](/articles/plot_phylogenetic_trees.qmd)
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