Auto-phylo v2

Auto-phylo v2 builds advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels, and identification of positively selected amino acid sites.

Key Features:

• Gene Annotation Modules: New modules for gene annotation support processing of non-annotated genomes.
• BLAST Search Algorithms: Additional BLAST search algorithms enable sequence similarity searches.
• Multiple Sequence Alignment Methods: Further multiple sequence alignment methods are supported for aligning sequences.
• Reference Sequence Integration: Reference sequences from public databases can be added to analyses.
• Tree Rooting Methods: Additional tree rooting methods are available for phylogenetic tree construction.
• Synonymous and Nonsynonymous Substitution Rate Estimation: The pipeline estimates rates of synonymous and nonsynonymous substitutions.
• Positive Selection Detection: The pipeline identifies positively selected amino acid sites.

Scientific Applications:

• S-RNase Specificity Inference: Pipelines identify amino acid sites under positive selection that determine S-RNase specificity, critical for cross-based breeding and establishment of pollination requirements.
• Gene and Gene Family Evolution: Phylogenetic inferences address biological questions regarding the evolution of genes and gene families from large-scale genome sequence data.
• Prunus Genome Analysis: Pipelines process non-annotated Prunus genomes combined with public database sequences for positive selection analysis.

Methodology:

The software employs automated pipeline construction incorporating gene annotation, BLAST searches, multiple sequence alignment, reference sequence addition, tree rooting, estimation of synonymous and nonsynonymous substitution rates, and detection of positively selected amino acid sites.