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SEGUL

MAF Summary

Summarize Multiple Alignment Format (MAF) files: the number of blocks, the alignment length, how much of the reference genome each species covers, and the proportion of gaps. Use it to check whole-genome alignments before converting them.

Quick example

Section titled “Quick example”

Using the genome.maf file from the MAF conversion example:

Terminal window
segul maf summary --input genome.maf

SEGUL writes two files to Maf-Summary. maf_summary_per_species.csv has one row per species:

path,name,blocks_present,block_proportion,aligned_columns,bases,gaps,gap_proportion,n_count,ref_bases_covered,ref_coverage
genome.maf,hg38,2,1.0000,17,15,2,0.1176,0,15,1.0000
genome.maf,mm10,2,1.0000,17,15,2,0.1176,0,15,1.0000
genome.maf,panTro6,1,0.5000,12,12,0,0.0000,0,10,0.6667

panTro6 is in one of the two blocks and aligns to 10 of the 15 reference bases.

SEGUL reads blocks the same way as the conversion: it names samples after their assembly (hg38.chr1 becomes hg38), uses the forward strand of the reference, and reads gzipped files directly. See how SEGUL reads MAF blocks.

Per-file summary

Section titled “Per-file summary”

maf_summary_per_file.csv has one row per MAF file:

Column Description
path MAF file
ref_species Reference species
blocks Blocks with a reference sequence
blocks_no_ref Blocks without a reference sequence (not included in other columns)
species Number of species
ref_chromosomes Number of reference chromosomes
ref_chrom_size_total Total length of those chromosomes
ref_bases Reference bases in all blocks
ref_genome_coverage ref_bases divided by ref_chrom_size_total
aligned_columns Total alignment length of all blocks
mean_block_columns Mean alignment length of a block
min_block_columns Shortest block alignment
max_block_columns Longest block alignment
mean_block_ref_len Mean reference bases in a block
mean_species_per_block Mean number of species in a block
mean_score Mean score of blocks with a score. Empty if no block has a score
gap_proportion Gaps (-) divided by all characters
duplicate_rows Rows dropped because a species appeared more than once in a block

Overlapping blocks are counted each time they appear, so ref_genome_coverage can be higher than the share of the genome that is covered. Very small values are written in scientific notation, such as 3.5952e-7.

Per-species summary

Section titled “Per-species summary”

maf_summary_per_species.csv has one row per species in each file. The reference comes first, followed by the other species in alphabetical order.

Column Description
path MAF file, or all for every file combined
name Species
blocks_present Blocks with the species
block_proportion blocks_present divided by the number of blocks
aligned_columns Total alignment length of the blocks with the species
bases Characters other than gaps
gaps Gaps (-)
gap_proportion gaps divided by aligned_columns
n_count Unknown bases (N and ?)
ref_bases_covered Reference bases aligned to a base of the species
ref_coverage ref_bases_covered divided by the reference bases of all blocks

With more than one input file, SEGUL adds rows with path set to all that combine every file.

All options

Section titled “All options”
Option Description
-d, --dir Directory with .maf and .maf.gz files. Subdirectories are not searched
-i, --input MAF files
--ref-species Reference species. Default: the first species in the first block
--species Species to report, comma-separated
--species-file File of species to report, one per line
--full-source-name Use full MAF source names as sample names
-o, --output Output directory. Default: Maf-Summary
--prefix Prefix of the output files. Default: maf_summary
--force Overwrite an existing output directory
--log Log file path. Default: segul.log

For example, to summarize every MAF file in a directory and name the output files primates_per_file.csv and primates_per_species.csv:

Terminal window
segul maf summary --dir maf/ --prefix primates

Copyright © 2026 H. Handika & J. A. Esselstyn.