BASE

BASE integrates non-ubiquitous orthologous gene groups into comparative genomics selection analyses to estimate dN/dS (ω) across coding sequences.

Key Features:

• Inclusion of non-ubiquitous orthogroups: Incorporates orthologous groups that are not ubiquitous across all species, enabling analysis of genes absent from some taxa.
• Support for non-single-copy orthogroups: Processes orthogroups that are not single-copy, accommodating multi-copy gene families.
• CodeML integration: Uses the CodeML framework to estimate selection pressures.
• dN/dS (ω) estimation: Estimates the dN/dS ratio (ω) on coding sequences at both site-specific and phylogenetic levels.
• Automated orthogroup processing: Automates processing of orthogroups for downstream selection analyses.
• Scalability: Designed to scale to large datasets and diverse gene groups produced by modern sequencing technologies.

Scientific Applications:

• Expanded selection regime analyses: Enables inclusion of non-ubiquitous orthogroups to increase genomic coverage in selection studies.
• Assessment of selective pressures: Assesses selective pressures across sites and phylogenetic branches using dN/dS (ω) estimates from CodeML.
• Comparative genomics across incomplete gene sets: Integrates genes absent in some lineages to investigate evolutionary dynamics across species.
• Orthogroup-level evolutionary inference: Facilitates analysis of evolutionary patterns at the orthogroup level across multiple species.

Methodology:

BASE leverages CodeML to estimate dN/dS (ω) on coding sequences and automates processing of orthologous groups, including non-single-copy and non-ubiquitous gene sets, for site-specific and phylogenetic-level analyses.