isect_mercator_alignment_gff command not found

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

Introduction

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

isect_mercator_alignment_gff: command not found

or when using sudo you get the following error message

sudo: isect_mercator_alignment_gff: command not found

Solutions to isect_mercator_alignment_gff: command not found

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

In Ubuntu isect_mercator_alignment_gff is provided by fsa package.

fsa is:

FSA is a probabilistic multiple sequence alignment algorithm which uses a “distance-based” approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz.

FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments:

  • FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This “query-specific learning” alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints.
  • FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy.
  • FSA can quickly align very long sequences using the “anchor annealing” technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above.
  • The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned

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

sudo apt-get -y install fsa

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

You can also use apt command to install fsa.

sudo apt -y install fsa

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

sudo aptitude install fsa

Summary

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