bppalnoptim command not found

In this troubleshooting guide we learn how to fix bppalnoptim command not found error message

Introduction

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

bppalnoptim: command not found

or when using sudo you get the following error message

sudo: bppalnoptim: command not found

Solutions to bppalnoptim: command not found

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

In Ubuntu bppalnoptim is provided by physamp package.

physamp is:

The PhySamp package currently contains two programs: bppphysamp, which samples sequences according to their similarity, and bppalnoptim, which samples a sequence alignment by removing sequences in order to maximize the number of sites suitable for a given analysis. The bppalnoptim program has three running modes:

  • Interactive: the user will be iteratively proposed a set of choices for sequence removal, with their corresponding site gains. The procedure stops when the user does not want to remove more sequences, and the resulting filtered alignment is written.
  • Automatic: the user enters an a priori criterion for stopping the filtering procedure (for instance a minimum number of sequences to keep).
  • Diagnostic: this mode allows one to plot the trade-off curve, by showing the site gain as a function of the number of removed sequences.

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

sudo apt-get -y install physamp

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

You can also use apt command to install physamp.

sudo apt -y install physamp

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

sudo aptitude install physamp

Summary

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