alignment-distances command not found

Introduction

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

alignment-distances: command not found

or when using sudo you get the following error message

sudo: alignment-distances: command not found

Solutions to alignment-distances: command not found

How To Fix alignment-distances: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu alignment-distances is provided by bali-phy package.

bali-phy is:

BAli-Phy estimates multiple sequence alignments and evolutionary trees from unaligned DNA, amino acid, or codon sequences. BAli-Phy uses MCMC to estimate evolutionary trees, positive selection, and branch lengths while averaging over alternative alignments. BAli-Phy can display alignment ambiguity graphically in an alignment uncertainty (AU) plot.

BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes and BEAST) using substitution models like GTR+gamma. BAli-Phy automatically estimates relative rates for each gene.

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

sudo apt-get -y install bali-phy

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

You can also use apt command to install bali-phy.

sudo apt -y install bali-phy

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

sudo aptitude install bali-phy

Summary

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