stem-rate

Table of Contents

• Installation
• Usage
  • Command Line Interface
• Contributors
• License

Installation

To install stem-rate, you can use pip:

pip install stem-rate

Usage

Command Line Interface

You can use stem-rate from the command line to add a fixed local clock stem model to BEAST1 XML files.

Basic usage

stem_rate flc --xml "your_input.xml" --stem "stem_value" --output "your_output.xml"

Arguments and Options

• --xml, -x: Path to the BEAST XML file.
• --stem, -s: Group sequences containing this value to define a stem.
• --fasta, -f (Optional): Sequences to add to XML in FASTA format. Dates must be in decimal year format.
• --delimiter, -d (Optional): Delimiter for date in FASTA header. Default is |.
• --position, -p (Optional): Position of date in FASTA header. Default is -1.
• --output, -o: Path to the output BEAST XML file.
• --version, -v (Optional): Print the version and exit.

For example, if you want to add sequences from a FASTA file and specify a date delimiter, you can run:

stem_rate flc --xml "your_input.xml" --stem "stem_value" --fasta "your_fasta.fasta" --delimiter "|" --position -1 --output "your_output.xml"

Contributors

• Wytamma Wirth

License

stem-rate is distributed under the terms of the MIT license.