Liger is a fast, composable concatenation tool that creates supermatrices from multiple FASTA alignments. It runs in two modes:

• Exact match (default): headers must match exactly across files, like FASconCAT and AMAS.
• Smart match (-a alias.txt): pass an alias list of clean output names that get matched to messy input headers via case-insensitive substring search. Underscores in aliases match spaces in headers, so Mus_musculus finds AB123.1 Mus musculus COX1 gene, partial cds. Longer aliases match first to prevent partial collisions. The alias list doubles as a rename map — input headers contain metadata, output gets clean names. Requires -l for a provenance TSV that records exactly which original header matched each alias.

Liger auto-detects DNA vs amino acid data per gene and adjusts missing characters and partition labels accordingly. FASTA output goes to stdout, partition boundaries to stderr in RAxML/IQ-TREE format by default. NEXUS bundles everything into one file.

Liger is also available as the concat subcommand in phylo.

Liger was benchmarked against AMAS, FASconCAT-G, PhyKit, pxcat, and SeqKit across combinations of 10–1,000 taxa and 10–1,000 loci. Liger is the fastest tool at every scale, while maintaining moderate memory usage.

Requires Rust.

cargo install --git https://github.com/andrewbudge/Liger

To update to the latest version:

cargo install --force --git https://github.com/andrewbudge/Liger

The previous Go version (v1) is preserved in the v1-go/ directory.

liger [FLAGS] [INPUT FASTA FILES]

• -a, --alias — alias list for smart matching (clean output names that map to messy input headers)
• -l, --log — provenance TSV output file (required with -a)
• -f, --format — output format: fasta (default), nexus (also accepts n or nex)
• -m, --missing — override missing data character (default: N for DNA, X for amino acid, ? for mixed)
• -p, --partitions — partition format: raxml (default, also used by IQ-TREE) or nexus

$ liger gene1.fasta gene2.fasta > supermatrix.fasta
DNA, gene1.fasta = 1-500
DNA, gene2.fasta = 501-1000

$ cat alias.txt
Mus_musculus
Rattus_rattus
Xenopus_laevis

$ liger -a alias.txt -l prov.tsv gene1.fasta gene2.fasta > supermatrix.fasta
DNA, gene1.fasta = 1-4
DNA, gene2.fasta = 5-8

$ cat supermatrix.fasta
>Mus_musculus
ATCGATCG
>Rattus_rattus
ATCGNNNN
>Xenopus_laevis
NNNNATCG

$ cat prov.tsv
alias.txt   gene1.fasta gene2.fasta
Mus_musculus    AB123.1 Mus musculus gene1 cds  XM456.1 Mus musculus gene2 cds
Rattus_rattus   AB124.1 Rattus rattus gene1 cds MISSING
Xenopus_laevis  MISSING XM789.1 Xenopus laevis gene2 cds

$ liger -a alias.txt -l prov.tsv -f nexus gene1.fasta gene2.fasta
#NEXUS
BEGIN DATA;
  DIMENSIONS NTAX=3 NCHAR=8;
  FORMAT DATATYPE=DNA MISSING=N GAP=-;
  MATRIX
  Mus_musculus    ATCGATCG
  Rattus_rattus   ATCGNNNN
  Xenopus_laevis  NNNNATCG
;
END;
BEGIN SETS;
  CHARSET gene1.fasta = 1-4;
  CHARSET gene2.fasta = 5-8;
END;

Partitions always go to stderr so they can be piped or redirected.

# Default: RAxML/IQ-TREE format
$ liger dna_gene.fasta protein_gene.fasta > matrix.fasta
DNA, dna_gene.fasta = 1-500
WAG, protein_gene.fasta = 501-700

# NEXUS charset format
$ liger -p nexus dna_gene.fasta protein_gene.fasta > matrix.fasta
CHARSET dna_gene.fasta = 1-500;
CHARSET protein_gene.fasta = 501-700;

Liger v2 is a rewrite in Rust of the original Go tool (v1). Development is assisted by Claude (Anthropic), which serves as a teaching aid and coding partner. The design, domain knowledge, and direction are the author's own.

Andrew Budge