A translation-aware framework for alignment-free phylogenetics using machine learning

Features

Covary is a computational framework designed for large-scale biological sequence analysis, powered by TIPs-VF.

Alignment-free analysis

Translation-aware embeddings

Distance-based clustering

Phylogenetic resolution

Toolkits

Phylogenomic tools, data processing workflows and simulation pipelines that are built for Covary.

Mutagen-PX

A lightweight Python toolkit that simulates tumor-specific gene sequence profiles by applying patient mutation data from TCGA cohorts to a reference sequence. It recreates/simulates “mutated” FASTA outputs per patient, allowing comparative genomics and downstream mutational analyses.

Seed Aligner

A computationally-optimized tool that detects a common seed region across genetic sequences and reorders them to start at the same point. It standardizes FASTA inputs for Covary without performing full multiple sequence alignment.

Covary-encoder

A k-mer-derived, non-overlapping, and frequency-independent encoding logic. It represents genetic sequences based on the relative proximity and directional alignment of k-mer attributes while incorporating sequence, length, positional, and translation awareness.

Usage

Covary leverages alignment-free, translation-aware embeddings to compare, cluster, and analyze genetic sequences, enabling insights into phylogenetic relationships, functional divergence, and taxonomic resolution.

Perform large-scale phylogenomic analyses

Embed sequences with translation-aware context

Run fast, scalable exploratory workflows

Analyze sequences without alignment or gaps

Use Cases

Covary is suitable for use in solving a number of research questions.

Taxonomic studies

Covary provides alignment-free, translation-aware comparisons that help distinguish species, infer relatedness, and support phylogenetic analyses even across highly divergent sequences.

Pathogen detection

Covary can rapidly screen genetic sequences from clinical or environmental samples to identify viral, bacterial, or fungal pathogens without requiring multiple sequence alignment.

Metagenomic exploration

Covary enables fast, large-scale profiling of mixed microbial communities, helping researchers uncover taxonomic composition, detect rare organisms, and analyze functional divergence within complex datasets.