alignmentsfil

Alignmentsfil is a file format intended to store one or more sequence alignments, commonly used in bioinformatics but applicable to any sequential data such as text. It provides a lightweight, machine-readable representation designed for exchange between analysis tools and data repositories.

A typical alignmentsfil file begins with a header containing metadata such as version, creation date, and source. Each alignment record identifies the alignment by an id, specifies the type (pairwise or multiple), and lists the participating sequences along with coordinates, strand information, and an alignment score. Sequences may be embedded as aligned strings with gaps or referenced to external sequence records.

Fields commonly supported include alignment_id, type, reference_id, entries (one per sequence), start and end positions, strand, gap representation, percent_identity, and coverage. Optional annotations may describe methods used to generate the alignment or references to supporting data.

Uses include exchanging alignment data between tools, reformatting alignments for visualization, and feeding data into downstream analyses. Implementations typically provide parsers in multiple programming languages and may offer validation against a simple schema or support streaming processing for large datasets.

Alignmentsfil is described here as an example format used to illustrate how alignment data can be stored and exchanged. Its adoption varies by project, and many communities prefer other formats for large-scale work.

See also: sequence alignment, multiple sequence alignment, alignment formats.