SEGUL is an ultrafast and memory efficient command-line (cli) application for working with sequence alignments that typically done using interpreted programming languages, such as Python, R, or Perl. It is designed to handle genomic datasets, but just as capable for Sanger datasets. In our test using a dataset with 4060 UCE loci, for instance, compare to a program written using biopython library, SEGUL is >40x faster for alignment concatenation while using 3x less RAM space.
Available features:
Planned features:
Supported sequence formats:
All of the formats are supported in interleave and sequential.
Supported partition formats:
charset in the app)It is now in active development. Our goal is to provide as many functionalities possible for alignment manipulation tasks.
The program may work in any rust supported platform. Below is a list of operating system that we tested and is guaranteed to work:
If you already using a rust program and familiar with its toolchain, the best option is to install the app using cargo. If you are new to using a command line application, installing through cargo is also the easiest route (see details in the installation instruction). To install through cargo:
{Bash}
cargo install segul
You can also use the pre-compiled binary available in the release page. The installation is similar to any other single executable command line app, such as the phylogenetic programs IQ-Tree and RaXML. You only need to make sure the path to the app is registered in your environment variable, so that the app can be called from anywhere in your system (see instructions).
The program command structure is similar to git, gh-cli, or any other program that use subcommands. The program file name will be segul for Linux/MacOS and segul.exe for Windows.
{Bash}
[THE-PROGRAM-FILENAME] <SUBCOMMAND> [OPTIONS] <VALUES> <A-FLAG-IF-APPLICABLE>
To check for available subcommand:
{Bash}
segul --help
To check for available options and flags for each sub-command:
{Bash}
segul <SUBCOMMAND> --help
For example, to concat all the alignments in a directory named nexus-alignments:
{Bash}
segul concat --dir nexus-alignments --format nexus
It is also available in short options:
{Bash}
segul concat -d nexus-alignments -f nexus
The program outputs are the resulting files from each task and a log file. Most information that is printed to the terminal is written to the log file. Unlike the terminal output that we try to keep it clean and only show the most important information, the log file will also contain the dates, times, and the log level status. The program will append the log outputs to the same log file (named segul.log) each time you run the program if the file exist in the same directory. Rename this file or move it to a different folder if you would like to keep a different log file for each task.
:warning: Unlike the log file, for the other outputs, the app will over-write existing files with the same names: Careful in specifying the output file names. Future updates will prevent it.
We want the installation as flexible as possible. We offer three ways to install the program. Each of the options has its own advantages and disavantages.
The pre-compiled library is available at the release page. The typicall workflow is as folow:
See specific details below:
First, copy the link to the zip file in the release page. We provide two versions of the app for Linux. The zip file labeled with HPC is compiled using Red Hat Enterprise Linux Server 7.9 (Kernel Version 3.10). If you are running the program in HPC, you should use this version. The other version (labeled Linux only) is compiled using Ubuntu 20.04 LTS (Kernel version 5.8). You should use this if you are using more up to date Linux. Simply put, if you encounter GLIBC error, try using the HPC version. If the issue still persists, try install using cargo.
For MacOS, the executable is available for an Intel Mac. If you are using Apple silicon Macs (M1), may be best to install it through cargo.
Here, we use the version 0.3.1 as an example. You should replace the link with the most up to date version available in the release page.
```{Bash}
wget https://github.com/hhandika/segul/releases/download/v0.3.1/segul-MacOS-x86_64.zip ```
{Bash}
unzip segul-MacOS-x86_64.zip
{Bash}
chmod +x segul
If you would like the binary executable for all users:
{Bash}
chmod a+x segul
The next step is putting the binary in a folder registered in your path variable. It is always best to avoid registering too many paths in your environment variable. It will slow down your terminal startup if you do. If you already used a single executable cli app, the chance is that you may already have a folder registered in your path variable. Copy SEGUL executable to the folder. Then, try call SEGUL from anywhere in your system:
{Bash}
segul --version
It should show the SEGUL version number.
If you would like to setup a folder in your environment variable, take a look at simple-qc installation instruction.
The installation procedure is similar to the MacOS or Linux. After downloading the zip file for Windows and extracting it, you will setup your environment variable that point to the path where you will put the executable. Follow this amazing guideline from the stakoverflow to setup the environment variable. After setup, copy the segul.exe file to the folder.
This is the recommended option. Cargo will compile the program and fine-tuned it for your specific hardware. It also allows to easily updating the app. You will need the rust compiler toolchain. It requires rust version 1.5 or higher. Then, check if the toolchain installation successful:
{Bash}
cargo --version
It should show the cargo version number. Then, install the app:
{Bash}
cargo install segul
If you encounter a compiling issue, you may need to install a C-development tool. For Debian-based Linux distribution, such as Debian, Ubuntu, PopOS, etc., the easiest way is to install build-essential:
{Bash}
sudo apt install build-essential
For OpenSUSE:
{Bash}
zypper install -t pattern devel_basis
For Fedora:
{Bash}
sudo dnf groupinstall "Development Tools" "Development Libraries"
For Windows, you only need to install the GNU toolchain for rust. The installation should be straighforward using rustup. Rustup comes as a part of the rust-compiler toolchain. It should be available in your system at the same time as you install cargo.
{Bash}
rustup toolchain install stable-x86_64-pc-windows-gnu
Then set the GNU toolchain as the default compiler
{Bash}
rustup default stable-x86_64-pc-windows-gnu
Try to install SEGUL again:
{Bash}
cargo install segul
You will need rust compiler toolchain. To install the development version for any supported platform:
{Bash}
cargo install --git https://github.com/hhandika/segul.git
You should have SEGUL ready to use.
It is equivalent to:
```{Bash} git clone https://github.com/hhandika/segul
cd segul/
cargo build --release ```
The different is that, for the latter, the executable will be in the segul repository: /target/release/segul. Copy the segul binary and then add it to your environment path folder.
Then, try to call SEGUL:
{Bash}
segul --version
```{Bash}
USAGE:
segul
FLAGS: -h, --help Prints help information -V, --version Prints version information
SUBCOMMANDS: concat Concatenates alignments convert Converts sequence formats filter Filter alignments with specified min taxon completeness, alignment length, or parsimony informative sites help Prints this message or the help of the given subcommand(s) id Gets sample ids from multiple alignments summary Gets alignment summary stats ```
More detailed instructions coming soon...