You can use SFTP through an FTP client like filezilla. There are command line clients as well but I'm not sure if you prefer command line or not. Use port 22 on the destination host.

If you want to transfer over SSH, the scp command is what you want.

For example, if you're on the host with the FASTA file and you want to transfer it to your destination host:

scp /path/to/my.fasta username@my.remote.host:/destination/path/

This will copy my.fasta to the directory /destination/path/ on the remote host.

There is a very simple command:

scp from to

Example to supercomputer:

scp /path/to/your/file username@132.343.12.3:/path/to/your/destination/on/supercomputer
scp /home/acresearch/desktop/uniprot90 acresearch@castor:/home/acresearch/databses

Example from supercomputer:

scp username@132.343.12.3:/path/from/your/supercomputer /path/to/your/computer/destination
scp acresearch@castor:/home/acresearch/databses/uniprot90 /home/acresearch/desktop

Another way:

If you understand how to SSH, then you will understand how to SFTP. It is the same concept except for file transfer. You use put to upload and get to download