auto-phylo

auto-phylo-pipeliner facilitates the creation and execution of automated pipelines for phylogenetic inference, estimation of variability levels, and identification of positively selected amino acid sites.

Key Features:

• Pipeline Creation: Supports building automated pipelines for phylogenetic analysis from genome sequence data.
• Gene Annotation: Includes modules for gene annotation to process non-annotated genomes.
• BLAST Search Integration: Incorporates additional BLAST search algorithms for sequence identification.
• Multiple Sequence Alignment: Supports further multiple sequence alignment methods beyond previous versions.
• Reference Sequence Addition: Enables adding reference sequences to analyses.
• Tree Rooting: Includes additional tree rooting methods for phylogenetic inference.
• Synonymous and Nonsynonymous Substitution Rates: Estimates rates of synonymous and nonsynonymous substitutions.
• Positive Selection Detection: Identifies positively selected amino acid sites in protein sequences.

Scientific Applications:

• S-RNase Specificity Inference: Identifies amino acid sites under positive selection that determine S-RNase specificity for cross-based breeding and pollination requirement establishment.
• Gene and Gene Family Evolution: Addresses biological questions regarding the evolution of genes and gene families from large-scale genome sequence data.
• Prunus Genome Analysis: Processes non-annotated Prunus genomes combined with public database sequences for phylogenetic inference.

Methodology:

The computational methods include gene annotation, BLAST search algorithms, multiple sequence alignment, reference sequence addition, tree rooting, estimation of synonymous and nonsynonymous substitution rates, and identification of positively selected amino acid sites.