phyml command not found
Introduction
When you run more command in linux terminal / console, you get the following error message
phyml: command not found
or when using sudo you get the following error message
sudo: phyml: command not found
Solutions to phyml: command not found
How To Fix phyml: command not found in Ubuntu / Debian / Kali Linux / Raspbian
In Ubuntu phyml is provided by phyml package.
phyml is:
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test).
PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long.
This package also includes PhyTime.
To fix this problem, we can install more using the command below.
sudo apt-get -y install phyml
This command might take some time to finish depending on your machine internet connection.
You can also use apt command to install phyml.
sudo apt -y install phyml
Or if you have aptitude installed you can use the following command.
sudo aptitude install phyml
Summary
In this tutorial we learn how to fix phyml command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.