PhyloToL

PhyloToL performs phylogenomic analyses across diverse eukaryotic lineages by integrating high-throughput sequencing (HTS) data to generate multiple sequence alignments (MSAs) and infer gene phylogenies for comparative and evolutionary studies.

Key Features:

• Integration with HTS data: Incorporates high-throughput sequencing (HTS) datasets for phylogenomic analysis.
• Automation of MSAs and gene trees: Automates production of multiple sequence alignments (MSAs) and inference of gene trees.
• Contaminant identification and removal: Detects and removes contaminants and addresses HTS errors such as substitutions to improve data quality.
• Flexibility and scalability: Scales to large, deep-time analyses (e.g., >100 million years) across diverse taxa.
• Benchmarked homology assessment: Homology assessment and gene-family inference benchmarked against OrthoMCL and studies of bacterial and eukaryotic organellar outer membrane pore-forming protein superfamilies.

Scientific Applications:

• Stop codon usage analysis: Analysis of stop codon usage in Ciliophora.
• Contamination detection: Identification of contamination in taxon- and gene-rich databases.
• Evolutionary history exploration: Investigation of chromosome evolution in the kinetoplastid parasite Trypanosoma brucei (agent of African sleeping sickness).

Methodology:

Integrates HTS data, automates MSAs and gene-tree inference, identifies and removes contaminants and common HTS errors, and supports integration with PhyloChromoMap and iGTP for downstream phylogeny and gene-family analyses.