PairwiseAlignmentResult.php
Immutable value object describing the outcome of a pairwise sequence alignment Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 7 October 2026
Table of Contents
Classes
- PairwiseAlignmentResult
- alignedFirst and alignedSecond are the two input sequences with '-' gap symbols inserted so they share the same length, column by column. first/secondStart and first/secondEnd are zero-based, inclusive positions in the ORIGINAL, ungapped sequences that the aligned region covers : for a global alignment (Needleman-Wunsch) this always spans the whole of both sequences, but the same shape is reused by local alignment (Smith-Waterman), where it identifies the aligned subsequence.