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.
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)
- Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/datatypes/
- Common datatypes explained https://galaxyproject.org/learn/custom-genomes/
Galaxy FAQs, including the above: https://galaxyproject.org/support/
Galaxy Tutorials: https://galaxyproject.org/learn/
There are two Public usegalaxy* servers with this tool installed. Galaxy Europe: https://usegalaxy.eu and Galaxy Main https://usegalaxy.org: 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:
>seq1 GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT >seq2 GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT
Thanks! Jen, Galaxy team