The Alignment tab settings control the algorithm for aligning rows in the comparison.
Pick Sorted alignment to reorder the rows based on their keys before aligning them.
Pick Unaligned to compare files without aligning rows based on their content.
Pick Standard alignment to align the files by comparing successively smaller sections of each file. Parts of the alignment can be shown before the entire comparison is finished.
Pick Myers O(ND) alignment to align the files using a common LCS (Longest Common Subsequence) algorithm. This can give better matches in certain cases, such as large inserts or when the files contain a lot of repeating text. Since files are compared all at once, larger file scans take much longer than the standard method, and the files are not displayed until the comparison is complete. It does not support similarity comparisons, so mismatches will be grouped in blocks.
Pick Patience Diff alignment to align the files using Bram Cohen's algorithm.
Mark the Use closeness matching checkbox to attempt to align the remaining mismatched rows based on their similarity.