Introduction

The goals of SEGUL CLI are to be easy to use for beginners and to provide powerful options for experienced users. Some common arguments have short options. Some of them also have default values when they are possible and safe to have. This way, we will save time typing the commands.

Several considerations before using segul:

1. The SEGUL CLI has two input options (--dir and --input). The --dir option tells SEGUL to find matching files for the task in the input directory. It will search recursively across the input directory. The --input option relies on users or the operating system to provide the paths to the input files. See command options for details.
2. The SEGUL CLI datatype is DNA by default. Use the --datatype aa option if your input file contains amino acid sequences.
3. Except for computing alignment statistics, you can pass --datatype ignore. This will speed up the processing time by up to 40 percent. Use this option carefully. It is safe for DNA sequences. It is only safe for amino acid sequences when the output is not in nexus format. You can learn more in the command options.
4. The command examples below are for Unix-like OS, such as Linux, Windows Subsystem for Linux, and MacOS. If you run segul natively on Windows, the program name will be segul.exe.
5. SEGUL CLI has default output directories for each task. You can specify the output directory by using the --output or -o argument.
6. For some tasks, such as alignment concatenation and summary statistics, you can use the --prefix argument to specify the prefix of the output files.

Note

If you use PowerShell 7 on Windows, you can type segul just like Unix-like OS.