Haplowser

Haplowser facilitates comparative visualization and analysis of haplotypes across genomes to characterize genetic variation in personal human genomes and metagenomes.

Key Features:

• Comparative Visualization: Global alignment and browser-style comparison of multiple haplotypes to reveal evolutionary relationships and variation across species and metagenomic samples.
• Whole-Genome Alignments: Uses whole-genome alignments to perform comprehensive, genome-wide comparisons of haplotypes.
• Functional Annotation Integration: Maps functional annotations onto conserved regions of aligned haplotypes and quantifies associations, presenting results as pie charts.
• Custom Track Support: Allows projection of custom tracks onto haplotypes and saves annotations and custom tracks in FASTA format for downstream analyses.

Scientific Applications:

• Evolutionary biology: Comparative haplotype analysis to infer evolutionary relationships and conserved sequence features.
• Genomics: Identification and annotation of functional genomic elements through alignment-conserved regions and integrated annotations.
• Metagenomics: Comparative analysis of haplotypes within metagenomic samples to detect biologically significant sequences and diversity.
• Personal genomics: Analysis of haplotype variation in personal human genomes to characterize individual genetic differences.

Methodology:

Haplowser employs whole-genome alignments to compare haplotypes and integrates these alignments with functional annotations and custom tracks.