halSynteny

halSynteny reconstructs synteny blocks from HAL-format whole-genome alignments, including multi-hundred-way reference-free vertebrate Cactus alignments, to identify conserved syntenic regions and chromosomal rearrangements for comparative genomics.

Key Features:

• Pairwise alignment processing: Processes pairwise alignment blocks across any pair of genomes within a large multiple-genome alignment.
• Reference-free whole-genome alignment support: Operates on reference-free whole-genome alignments to enable high-resolution cross-species homology detection.
• Binary-format handling: Handles very large multiple alignments stored in binary format to support large-scale datasets.
• Synteny identification: Enables rapid identification of synteny across multiple full-genome alignments.
• Reconstruction of rearrangements: Reconstructs chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks.
• Implementation: Implemented in C++11 as part of halTools within the HAL (Hierarchical Alignment) comparative genomics suite.

Scientific Applications:

• Large-scale comparative genomics: Applied in large-scale sequencing projects with high-quality full-genome data to reconstruct syntenic blocks across species.
• Genome rearrangement analysis: Supports reconstruction and analysis of chromosomal exchanges and rearrangements to study structural genome evolution.
• Evolutionary and architectural inference: Facilitates investigation of conserved syntenic regions to infer genomic architecture and evolutionary relationships.

Methodology:

Processes pairwise alignment blocks from HAL multiple-genome alignments stored in binary format, including reference-free Cactus multi-hundred-way vertebrate alignments, to produce synteny blocks; implemented in C++11 as part of halTools.