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