compare_2_profiles.pl command not found

In this troubleshooting guide we learn how to fix compare_2_profiles.pl command not found error message

Introduction

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

compare_2_profiles.pl: command not found

or when using sudo you get the following error message

sudo: compare_2_profiles.pl: command not found

Solutions to compare_2_profiles.pl: command not found

How To Fix compare_2_profiles.pl: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu compare_2_profiles.pl is provided by pftools package.

pftools is:

The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases.

File formats used by the pftools

  • Generalized profiles format and syntax.
  • The multiple sequence alignment format (PSA).
  • The extended header multiple sequence alignment format (XPSA).

Programs to build generalized profiles pfmake Build a profile from a multiple sequence alignment. pfscale Fit parameters of an extreme-value distribution to a profile score list. pfw Weight sequences of a multiple sequence alignment to correct for sampling bias.

Programs to search with generalized profiles pfsearch / pfsearchV3 Search a protein or DNA sequence library for sequence segments matching a profile (V3 is the new version of this tool). pfscan Scan a protein or DNA sequence with a profile library

Conversion programs psa2msa Reformat PSA file to Pearson/Fasta multiple sequence alignment file. ptof Convert a protein profile into a frame-search profile to search DNA sequences. To be used with 2ft. 2ft Converts both strands of DNA into so-called interleaved frame-translated DNA sequences to search with protein profiles. To be used with ptof. 6ft Translates all six reading frames of a double-stranded DNA sequence into individual protein sequences. pfgtop Convert a profile in GCG format into PROSITE format. pfhtop Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile. ptoh Converts a generalized profile into an approximately equivalent HMM profile in HMMER1 format (can be read by the hmmconvert program from the HMMER2 package).

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

sudo apt-get -y install pftools

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

You can also use apt command to install pftools.

sudo apt -y install pftools

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

sudo aptitude install pftools

Summary

In this tutorial we learn how to fix compare_2_profiles.pl command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.