📄️ Overview
The goals of segul are to be easy to use for non-tech-savvy users and provides 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.
📄️ Command Options
segul command is structured this way:
📄️ Alignment Concatenation
segul provides an easy way to concat multiple alignments and generate the partition setting at the same time.
📄️ Alignment Conversion
Segul can convert a single file, multiple file in the same directory, or multiple files in multiple directory.
📄️ Alignment Filtering
segul provides multiple ways to filter alignments:
📄️ Alignment Partition Conversion
segul can convert a single and multiple partition files in multiple folders. You can also use this function to extract partition embedded in NEXUS sequence files.
📄️ Alignment Splitting
To split an alignment, you need two input files: the concatenated alignment and the partition file. If you skip inputting partition file, the app will assume the partition is embedded in the alignment file.
📄️ Alignment Summary
segul generates different summary statistics for DNA and amino acid sequences. By default, the datatype is set to DNA sequence. In general, the command is as below:
📄️ Genomic Summary
Since version 0.19.0, segul can calculate summary statistics for raw reads and contiguous sequences.
📄️ Sequence ID Extraction
Often, we need to know what are the taxa we in our dataset. The simplest command would be:
📄️ Sequence ID Mapping
To map the distribution of your samples across your dataset, you only need to pass --map flag in the finding unique IDs command:
📄️ Sequence ID Renaming
segul provide an easy way to rename sequence IDs across all your alignments. To use this function, segul require a list of the original IDs and the the name IDs that it needs to change to. The input IDs can be written in a tabulated format as a comma-delimited file (.csv) or a tab-delimited file (.tsv).
📄️ Sequence Extraction
segul can extract sequences in a collection of alignments based on the sequence ID. You can input the sequence ID in three ways:
📄️ Sequence Removal
Based on a list of IDs, you can remove sequences in a collection of alignments. This feature is the opposite of segul extract feature. It is faster than segul extract if you remove less than a half of the sequences.
📄️ Sequence Translation
To translate dna alignment to amino acid:
📄️ Log File
With the exception of the spinning emoji and the program progress messages, all the terminal output is written to segul.log file saved in the current working directory. In the log output, however, it is also include the time and the log status. For example, our terminal output is as follow: