Question: How to align sequences with MAFFT
gravatar for winklma01
14 days ago by
winklma010 wrote:

I want to align two FASTA sequences. I am trying to use MAFFT , Multialign tool in Galaxy. Does this program want two sequences next to each other in a FASTA file? It will not take two FASTA files to align the sequences from those two files. I have tried merging two FASTA files and inputting that merged file with no results.

ADD COMMENTlink modified 13 days ago by Jennifer Hillman Jackson25k • written 14 days ago by winklma010
gravatar for Jennifer Hillman Jackson
13 days ago by
United States
Jennifer Hillman Jackson25k wrote:


The two sequences should be stacked one on top of each other (tool: Concatenate), in strict fasta format (tool: NormalizeFasta), and have unique identifiers.

FAQs for Custom genomes/fasta -- the formatting rules also apply to most other tools that accept fasta format inputs (for any input parameter)

Galaxy FAQs, including the above:

Galaxy Tutorials:

There are two Public usegalaxy* servers with this tool installed. Galaxy Europe: and Galaxy Main MAFFT Multiple alignment program for amino acid or nucleotide sequences (Galaxy Version 7.221.3).

I just tested it with two very small sequences, that had some overlap, in proper fasta format, using all defaults, and achieved a successful result for both FASTA and ClustalW output (Phylip output is not supported at this server, as noted under the output format selection help, and will trigger a job failure). If you want to compare your input data to the test data I used, this is the content of the fasta:


Thanks! Jen, Galaxy team

ADD COMMENTlink modified 13 days ago • written 13 days ago by Jennifer Hillman Jackson25k
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