pair_align: command not found

Have You tried accessing the binary with the full path?

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

[root@server ~]# echo $PATH

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/pair_align - from package: seqan-apps
/usr/lib/seqan/bin/pair_align - from package: seqan-apps

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