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Updated: Jun 5, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more.

Nelson R Salinas¹, Gil Eshel², Gloria M Coruzzi²

¹Lewis B. and Dorothy Cullman Program for Molecular Systematics The New York Botanical Garden, Bronx New York USA.

Applications in Plant Sciences

|December 4, 2024

Summary

This summary is machine-generated.

A new Python script, BAD2matrix, simplifies phylogenomic matrix construction. It automates common steps for DNA, amino acid, and morphological data, streamlining complex analyses.

Keywords:

concatenation gene content gene presence/absence indel coding morphology occupancy filtering phylogenomics reduced amino acid alphabets

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Last Updated: Jun 5, 2025

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Published on: August 14, 2018

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A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Phylogenomic matrix construction involves multiple complex steps.
Existing software often requires multiple programs for these tasks.
There is a need for integrated tools to simplify phylogenomic analyses.

Purpose of the Study:

To develop a single program for comprehensive phylogenomic matrix production.
To automate key steps in creating phylogenomic datasets.
To provide a user-friendly tool for researchers in evolutionary biology.

Main Methods:

Developed BAD2matrix, a Python script for phylogenomic matrix construction.
The script handles DNA, amino acid, and morphological data.
It integrates common steps like sequence concatenation, indel coding, and occupancy filtering.

Main Results:

BAD2matrix successfully automates multiple phylogenomic matrix production steps.
The script is compatible with UNIX-like environments.
It simplifies complex phylogenomic data preparation pipelines.

Conclusions:

BAD2matrix offers a unified solution for phylogenomic matrix construction.
The script enhances efficiency in bioinformatics workflows.
It is available under a GNU General Public License v2.