MSWAT---a Multiple Sequence Web viewer and Alignment Tool for phylogeny
Welcome to MSWAT Please Download Mozilla FireFox if you are using a MAC since MSWAT does not work with Safari.If you are using a PC, you can use either Internet Explorer or Mozilla FireFox. If you have any questions or suggestions regarding this tool, please contact Zhengqiu Cai at or Robert K. Jansen at
What does MSWAT do? MSWAT conducts multiple sequence alignment for phylogeny and molecular evolutionary comparisons. It was initially designed to align shared genes from completely sequenced chloroplast genomes (see Cai et al. BMC Evol Biol. 2006; 6: 77 for an example). MSWAT has been used to generate an alignment for 81 chloroplast genes for 64 taxa (see Jansen, R. K et al. PNAS 104 (49), 19369-19374). It can be used to expand this data matrix by adding chloroplast genomes. It can also be used to align any sequences from other genomes.
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81 shared chloroplast genes Show the list of genes
61 shared chloroplast genes(34 genomes)
61 shared chloroplast genes
Any nucleotide sequences
How does MSWAT work? MSWAT uses fasta-formatted nucleotide sequence files as input. All protein-coding nucleotide sequences in the input files are translated into amino acid sequences, which are aligned using MUSCLE and/or ClustalW, followed by manual adjustments, and then nucleotide sequences of these genes are aligned by constraining them to the aligned amino acid sequences. Multiple files of different formats with character sets for phylogenetic analyses are generated after nucleotide sequence alignment is completed.
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How to use MSWAT? 1. Input file format
2. Input file creation
3. Alignment of new plastid genomes against an existing dataset
4. Starting a new aligned data matrix
5. Export the alignment
Download example files for testing this tool
Genbank | DOGMA | Chloroplast Genome Database | OGMP