Phyx

Phyx implements a suite of modular C++ command-line programs for processing sequence alignments, phylogenetic trees, and Markov Chain Monte Carlo (MCMC) logs to support phylogenetic and phylogenomic analyses using stream-centric, POSIX-compatible processing to minimize memory usage.

Key Features:

• Implementation Language: Implemented in C++.
• Modular Design: Each program performs a distinct task following the Unix/GNU/Linux command-line paradigm and supports integration via standard input/output streams.
• Stream-centric Processing: Processes data via streaming to minimize memory usage, typically holding only one tree or sequence in memory at a time.
• POSIX Compliance: Compatible with POSIX-compliant operating systems.

Scientific Applications:

• Phylogenomic Data Processing: Handling large-scale phylogenomic datasets for analysis and manipulation of sequence alignments and phylogenetic trees.
• MCMC and Simulation Analyses: Exploration, manipulation, analysis, and simulation of Markov Chain Monte Carlo (MCMC) logs and other phylogenetic objects.

Methodology:

Computations are performed via modular command-line programs using piping and stream-centric processing to enable complex workflows while minimizing memory overhead.