pal2nal.pl command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

pal2nal.pl: command not found

or when using sudo you get the following error message

sudo: pal2nal.pl: command not found

Solutions to pal2nal.pl: command not found

How To Fix pal2nal.pl: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu pal2nal.pl is provided by pal2nal package.

pal2nal is:

PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon-based DNA alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon-based DNA alignment can further be subjected to the calculation of synonymous (Ks) and non-synonymous (Ka) substitution rates.

To fix this problem, we can install more using the command below.

sudo apt-get -y install pal2nal

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install pal2nal.

sudo apt -y install pal2nal

Or if you have aptitude installed you can use the following command.

sudo aptitude install pal2nal

Summary

In this tutorial we learn how to fix pal2nal.pl command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.