Phykit Tools

Configuration File: phykit_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the phykit_tools.json configuration file.

Available Tools

phykit_batch_analysis (Type: PhyKITTool)

Run PhyKIT phylogenetics functions (treeness, saturation, dvmc, long_branch_score, total_tree_len…

phykit_batch_analysis tool specification

Tool Information:

  • Name: phykit_batch_analysis

  • Type: PhyKITTool

  • Description: Run PhyKIT phylogenetics functions (treeness, saturation, dvmc, long_branch_score, total_tree_length, parsimony_informative) on a directory of tree/alignment files. Returns summary statistics (mean, median, min, max). For long_branch_score, aggregates per-taxon values within each tree before cross-tree summary. Use for batch phylogenetic analyses comparing gene trees across organism groups.

Parameters:

  • operation (string) (required) single: one file, batch: all files in directory, gap_percentage: compute gap % across alignments

  • function (string) (optional) PhyKIT function to run

  • file ([‘string’, ‘null’]) (optional) Path to single tree/alignment file (for operation=single)

  • directory ([‘string’, ‘null’]) (optional) Directory containing tree/alignment files (for operation=batch or gap_percentage)

  • extension (string) (optional) File extension to match (default: .treefile for trees, .fa for alignments)

  • tree_directory ([‘string’, ‘null’]) (optional) Directory with paired tree files (for saturation function)

  • tree_extension (string) (optional) Tree file extension (default: .treefile)

  • per_tree_stat (string) (optional) How to summarize per-tree values for long_branch_score (default: mean)

Example Usage:

query = {
    "name": "phykit_batch_analysis",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)