prepareAlign command not found

Introduction

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

prepareAlign: command not found

or when using sudo you get the following error message

sudo: prepareAlign: command not found

Solutions to prepareAlign: command not found

How To Fix prepareAlign: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu prepareAlign is provided by augustus package.

augustus is:

AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes.

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

sudo apt-get -y install augustus

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

You can also use apt command to install augustus.

sudo apt -y install augustus

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

sudo aptitude install augustus

Summary

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