Alphabet

Each biological sequence is encoded using a valid set of characters to represent its composition. In the case of protein, this set consists of 20 canonical amino acids, with each amino acid being represented by a specific letter. The list includes: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y. Additionally, six non-standard amino acids, as detailed in Non-standard Residues section, also are included within the protein alphabet.
For DNA sequences, the alphabet comprises A, U, C, G along with non-standard nucleic acid, N. Similarly, in the case of RNA sequences, the alphabet consists of A, U, C, G along with non-standard nucleic acid, N.
Among the available tools for NEFF computation, while RaptorX and Conkit do not explicitly specify an alphabet, DeepMSA and rMSA operate within the protein alphabet. In contrast, Gremlin provides support for both protein and RNA (implicitly including DNA). Similarly, NEFFy covers a broad spectrum of biological sequences, encompassing proteins and nucleic acids, much like Gremlin.

Non-standard Residues

Non-standard residues are those that fall outside the standard set of residues, which typically includes N for DNAs and RNAs and X, B, J, O, U and Z for proteins. When it comes to NEFF computation and comparing the positions of a pair of sequences for similarity, there are various strategies available for handling these non-standard residues. One approach is to treat them as if they were standard amino acids, akin to the behavior exhibited by DeepMSA's symmetric version. Alternatively, they can be designated as gaps only when determining the permissible number of mismatches for each sequence, resembling the approach taken by DeepMSA's asymmetric option. Another option, similar to the practices of rMSA and Gremlin, involves categorizing them as gaps both in the calculation of number of allowable mismatches and in aligning corresponding positions for a pair of sequences. Among the tools, RaptorX and Conkit do not handle these residues. NEFFy is the only tool capable of handling these residues based on user preference,and its default option is to treat them as standard residues.

`make` Installation

To use the make command, follow the steps below according to your operating system:

macOS

The make command is not available by default on macOS. However, it can be easily installed by installing the Xcode Command Line Tools. You can do this by running the following command in the Terminal:

xcode-select --install

Linux

The make command is commonly available by default on many Linux distributions. If it's not installed, it can be easily added using the package manager of your distribution. For example:

On Debian-based systems (e.g., Ubuntu):
sudo apt-get install make
On Red Hat-based systems (e.g., Fedora):
sudo dnf install make
On Arch-based systems:
sudo pacman -S make

Windows

The make command is not available by default on Windows. However, it can be installed through several methods:

Using Cygwin:
- Install Cygwin from the Cygwin website.
- During the installation, select make from the package list.
Using GnuWin:
- Go to the GnuWin website.
- Download the make package setup executable (e.g., make-3.81.exe).
- Run the installer and follow the instructions to install make.
Using WSL (Windows Subsystem for Linux):
- Install WSL and a Linux distribution from the Microsoft Store (e.g., Ubuntu).
- Once the distribution is set up, you can use the package manager to install make as you would on a native Linux system.

Set Up Environment Variables:

After installing, add the make binary to your system’s PATH.
Open the Start Menu, search for "Environment Variables," and select "Edit the system environment variables."
In the System Properties window, click on the "Environment Variables" button.
In the Environment Variables window, find the "Path" variable in the "System variables" section, select it, and click "Edit."
Click "New" and add the path to the directory where make.exe was installed (e.g., C:\Program Files (x86)\GnuWin32\bin).
Click "OK" to close all the windows.

Verify the Installation:

Open a new Command Prompt window.
Type make --version and press Enter.
You should see the version information for make, confirming that it has been installed correctly.

By following these steps, you can have the make command available on macOS, Linux, and Windows, ensuring a consistent development environment across different operating systems.

For further assistance or inquiries, please contact the developer or create an issue in the GitHub repository.