parallel-fasta: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/parallel-fasta - from package: last-align

You may install the required package with command apt-get install {package}

Error in other languages:
parallel-fasta: bevel nie gevind nie
parallel-fasta: comandă negăsită
parallel-fasta: comando não encontrado
parallel-fasta: commande introuvable
parallel-fasta: command not found
parallel-fasta: käsku ei ole
parallel-fasta: không tìm thấy lệnh
parallel-fasta: komanda nerasta
parallel-fasta: Kommando nicht gefunden.
parallel-fasta: kommandot finns inte
parallel-fasta: komut yok
parallel-fasta: nie znaleziono polecenia
parallel-fasta: níor aimsíodh an t-ordú
parallel-fasta: no se encontró la orden
parallel-fasta: no s'ha trobat l'ordre
parallel-fasta: opdracht niet gevonden
parallel-fasta: parancs nem található
parallel-fasta: perintah tidak ditemukan
parallel-fasta: príkaz nenájdený
parallel-fasta: příkaz nenalezen
parallel-fasta: команда не найдена
parallel-fasta: командата не е открита
parallel-fasta: 命令找不到
parallel-fasta: コマンドが見つかりません