SEGUL

SEGUL is an ultrafast and efficient solution for alignment manipulation tasks 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 4x less RAM space.

Available features:

1. Converting alignments to different formats.
2. Concatenating alignments.
3. Filtering alignments based on minimal taxon completeness, alignment length, or numbers of parsimony informative sites.
4. Computing alignment summary statistics.
5. Getting sample IDs from a collection of alignments.

Planned features:

1. Filtering sequences from a collection of alignments based on user-defined IDs.
2. Converting dna sequences to amino acid and vice versa.

Supported sequence formats:

1. Nexus
2. Relaxed phylip
3. Fasta

The program support all formats in interleaved and sequential.

It is now in active development. Our goal is to provide as many functionalities possible for alignment manipulation tasks.

Installation

Supported operating system:

• Linux
• MacOS
• Windows
• Windows Sub-System for Linux

To install, you can donwload the executable in the release tab. Or install through Rust package manager, cargo. You will need the rust compiler tool-chain to install SEGUL. It requires rust version 1.5 or higher. Then, check if the tool-chain 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 the development tool necessary to compile the app. For Linux, install build-essential.

For Debian-based distributions, such as Debian, Ubuntu, PopOS, Linux Mint, etc:

{Bash} sudo apt install build-essential

For Windows:

```{Bash} rustup toolchain install stable-x86_64-pc-windows-gnu

then

rustup default stable-x86_64-pc-windows-gnu ```

To install the development version for any supported platform:

{Bash} cargo install --git https://github.com/hhandika/segul.git

Usages

Available command options

```{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...