| name | bioconductor-msa |
| description | The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any externa |
| when_to_use | Use when: Performing multiple sequence alignment of amino acid or nucleotide sequences using msa().; Generating highly customizable, publication-ready PDF visualizations of alignments using msaPrettyPrint().; Calculating consensus sequences and conservation scores using msaConsensusSequence() and msaConservationScore().. Not for: For aligning massive genomic datasets (e.g., whole genomes), use minimap2 because msa is designed for gene- or protein-scale alignments.; For basic pairwise sequence alignments, use pwalign because it is specifically built for pairwise comparisons. |
| user-invocable | false |
msa
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.44.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: Biostrings
- Imports: Rcpp, BiocGenerics, IRanges, S4Vectors
- System requirements: GNU make
- Install:
BiocManager::install("msa")
When to Use
- Performing multiple sequence alignment of amino acid or nucleotide sequences using
msa().
- Generating highly customizable, publication-ready PDF visualizations of alignments using
msaPrettyPrint().
- Calculating consensus sequences and conservation scores using
msaConsensusSequence() and msaConservationScore().
When NOT to Use
- For aligning massive genomic datasets (e.g., whole genomes), use
minimap2 because msa is designed for gene- or protein-scale alignments.
- For basic pairwise sequence alignments, use
pwalign because it is specifically built for pairwise comparisons.
Data Requirements
- Input Format: Unaligned DNA, RNA, or Amino Acid sequences.
- Structure: Loaded as an
AAStringSet (or similar XStringSet) using readAAStringSet().
Key Parameters
- output ("pdf"): Format for pretty-printing (e.g., "pdf", "asis").
- showNames ("none"): Controls the display of sequence names in the printed alignment.
- showLogo ("none"): Controls the display of the sequence logo (e.g., "top", "none").
- shadingMode ("similar"): Mode for color shading in the alignment (e.g., "similar", "functional").
- type ("upperlower"): Type of consensus sequence to generate.
- askForOverwrite (FALSE): Whether to prompt before overwriting existing files during PDF generation.
- gapVsGap (0): Score assigned to gap-versus-gap matches when calculating conservation scores.
Best Practices
- Use
unmasked() to retrieve the original alignment if a colmask() has been applied to hide specific columns.
- Convert alignments to other formats using
msaConvert() for downstream phylogenetic analysis (e.g., with seqinr or ape).
- Use
output="asis" in msaPrettyPrint() when integrating alignments into Sweave or knitr documents.
Common Pitfalls
- PDF Compilation Failures:
msaPrettyPrint() failing to compile PDFs; fix this by ensuring a working LaTeX system with the texshade.sty package is installed on your system path.
- Alignments Running Off Page: Large alignments running off the page in PDFs; fix this by splitting the alignment into chunks using
subseq() and printing them separately.
- Memory Exhaustion: Running ClustalW on thousands of sequences can consume excessive memory; fix this by switching to ClustalOmega for large datasets.
Alternatives
DECIPHER: A powerful Bioconductor package for sequence alignment, database management, and oligonucleotide design.ape: For phylogenetic analysis and basic sequence manipulation.seqinr: For biological sequence retrieval and analysis.
Citations
- Bodenhofer U, Bonatesta E, Horejs-Kainrath C, Hochreiter S. (2015) "msa: an R package for multiple sequence alignment." Bioinformatics.
References
Run this on BioMate
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