Table 1. Open in new tab Comparison of...

Format

Application scenarios

Structure

Pros

Cons

Type

Chain

Suitable for large-scale genome assembly and cross-species comparisons; Used to represent syntenic regions.

Links sets of alignment blocks that are homologous and ordered in both genomes.

Useful for long-range relationships and annotation transfer.

Lacks base-pair level detail, focusing more on structure.

Pairwise

PAF

Efficient in long-read sequencing for storing large genomic alignments.

Tab-delimited, includes basic alignment data like names, lengths, positions, and mapping quality.

Efficient with large, long-read datasets.

Omission of finer alignment details which may be crucial for certain analyses.

Pairwise

MAF

Best for comparative genomics across multiple species, phylogenetics, and evolutionary studies.

Contains blocks with alignments, each block starts with “a” and sequence lines start with “s.”

Excellent for multi-species alignments and detailed analysis.

Bulky and less efficient for very large datasets.

Multiple

Delta

Ideal for closely related genomes or small-scale differences; Used by MUMmer for basic differences between sequences.

Consists of a header and alignment blocks detailing insertions, deletions, and substitutions.

Compact and efficient for similar sequences.

Less suitable for complex rearrangements and lacks detailed visualization.

Pairwise

Table 1.

Comparison of the widely used genome alignment formats.

Format	Application scenarios	Structure	Pros	Cons	Type
Chain	Suitable for large-scale genome assembly and cross-species comparisons; Used to represent syntenic regions.	Links sets of alignment blocks that are homologous and ordered in both genomes.	Useful for long-range relationships and annotation transfer.	Lacks base-pair level detail, focusing more on structure.	Pairwise
PAF	Efficient in long-read sequencing for storing large genomic alignments.	Tab-delimited, includes basic alignment data like names, lengths, positions, and mapping quality.	Efficient with large, long-read datasets.	Omission of finer alignment details which may be crucial for certain analyses.	Pairwise
MAF	Best for comparative genomics across multiple species, phylogenetics, and evolutionary studies.	Contains blocks with alignments, each block starts with “a” and sequence lines start with “s.”	Excellent for multi-species alignments and detailed analysis.	Bulky and less efficient for very large datasets.	Multiple
Delta	Ideal for closely related genomes or small-scale differences; Used by MUMmer for basic differences between sequences.	Consists of a header and alignment blocks detailing insertions, deletions, and substitutions.	Compact and efficient for similar sequences.	Less suitable for complex rearrangements and lacks detailed visualization.	Pairwise

Format	Application scenarios	Structure	Pros	Cons	Type
Chain	Suitable for large-scale genome assembly and cross-species comparisons; Used to represent syntenic regions.	Links sets of alignment blocks that are homologous and ordered in both genomes.	Useful for long-range relationships and annotation transfer.	Lacks base-pair level detail, focusing more on structure.	Pairwise
PAF	Efficient in long-read sequencing for storing large genomic alignments.	Tab-delimited, includes basic alignment data like names, lengths, positions, and mapping quality.	Efficient with large, long-read datasets.	Omission of finer alignment details which may be crucial for certain analyses.	Pairwise
MAF	Best for comparative genomics across multiple species, phylogenetics, and evolutionary studies.	Contains blocks with alignments, each block starts with “a” and sequence lines start with “s.”	Excellent for multi-species alignments and detailed analysis.	Bulky and less efficient for very large datasets.	Multiple
Delta	Ideal for closely related genomes or small-scale differences; Used by MUMmer for basic differences between sequences.	Consists of a header and alignment blocks detailing insertions, deletions, and substitutions.	Compact and efficient for similar sequences.	Less suitable for complex rearrangements and lacks detailed visualization.	Pairwise