SISRS

SISRS identifies and selects phylogenetically informative genomic regions directly from next-generation whole-genome shotgun sequencing reads to enable phylogenetic inference without de novo genome assembly, multiple-genome alignment, or a reference genome.

Key Features:

• Reference-Free Analysis: Processes raw sequencing reads without requiring a reference genome, de novo whole-genome assembly, or multiple-genome alignment.
• Efficient Identification of Phylogenetically Informative Loci: Identifies numerous loci containing variable sites with phylogenetic signal from large-scale datasets, enabling marker discovery directly from reads.
• Application in Diverse Taxonomic Groups: Has been applied to apes and to placental mammals to identify thousands of variable sites used for phylogeny reconstruction.
• Robustness in Handling Missing Data: Produces reliable phylogenies across datasets with varying levels of missing data and recovered eight distinct phylogenies resolving basal relationships among mammals.

Scientific Applications:

• Phylogenetic reconstruction from whole-genome shotgun data: Provides loci and variable sites directly from whole-genome shotgun sequence data for phylogenetic analyses.
• Estimation of mammalian relationships: Has been used to estimate placental mammal phylogeny and resolve basal mammalian relationships.
• Evolutionary studies across diverse taxa: Supports evolutionary biology research across diverse taxa where traditional marker development is impractical.

Methodology:

Simultaneous identification and selection of genomic regions with phylogenetic signal directly from next-generation sequencing reads by processing raw whole-genome shotgun reads without de novo assembly, multiple-genome alignment, or a reference genome.