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The Multiple Sequence Alignment (MSA) of a gene family can be downloaded as a fasta file.

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The default MSA file contains amino acid sequences of all members in the gene family. When you prune the tree (remove genes of certain organisms), then download MSA, the MSA will exclude those pruned genes. Read more about the MSA


The fasta header is formatted as:

>UniProt ID|Organism full name|Gene ID


For example:

>A8J0U2|Chlamydomonas reinhardtii|CHLREDRAFT_196438