Cladekit is a lightweight, composable CLI phylogenetics toolkit. A single binary, Cladekit provides many subcommands that replace common chains of bash commands or a collection of individual programs in phylogenetic pipelines. Examples include header extraction, concatenation, and alignment quality control.

Note: Cladekit is under active development. Subcommands may change or be added as the project matures.

Requires Rust.

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

This builds the binary and adds cladekit to your PATH.

To update to the latest version:

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

Extract headers from FASTA files.

Example:

$ cladekit getheaders testdata/test_good.fasta
Sequence1
Sequence2
Sequence1

$ cladekit getheaders -u testdata/test_good.fasta
Sequence1
Sequence2

Concatenate multiple gene alignments into a supermatrix. Unlike other tools, input files can live anywhere and globs are accepted.

Concat 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 — a file of clean output names (one per line, e.g. Mus_musculus) 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 stay messy, output gets clean names. Requires -l for a provenance TSV that records exactly which original header matched each alias.

Concat 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.

Exact match — clean headers:

$ cladekit concat gene1.fasta gene2.fasta > supermatrix.fasta
DNA, gene1.fasta = 1-4
DNA, gene2.fasta = 5-8

Smart match — messy headers with an alias list:

$ cat alias.txt
Mus_musculus
Rattus_rattus
Xenopus_laevis

$ cladekit concat -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

NEXUS output:

$ cladekit concat -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;

Flags:

• -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: auto per data type — N for DNA, X for amino acid, ? for mixed)
• -p, --partitions — partition format: raxml (default, also used by IQ-TREE) or nexus

Get basic alignment statistics from FASTA files. Accepts multiple files via globs. Automatically detects DNA vs amino acid sequences.

Columns:

• file — filename (path stripped)
• sequences — number of sequences
• length — alignment length (NA if unaligned)
• type — DNA or AA (auto-detected, supports IUPAC ambiguity codes)
• gc_pct — GC content as a percentage of real bases (NA for amino acid data)
• missing_pct — percentage of gaps and unknown characters
• variable — sites with at least 2 different residues (excluding gaps/unknowns)
• variable_pct — variable sites as a percentage of alignment length
• informative — parsimony-informative sites (at least 2 residues each appearing 2+ times)
• informative_pct — informative sites as a percentage of alignment length

Example:

$ cladekit stats supermatrix.fasta proteins.fasta
file	sequences	length	type	gc_pct	missing_pct	variable	variable_pct	informative	informative_pct
supermatrix.fasta	3	8	DNA	50.0	33.3	0	0.0	0	0.0
proteins.fasta	4	20	AA	NA	0.0	3	15.0	2	10.0

Flags:

• -d, --detailed — per-sequence statistics (header, length, GC%, missingness)
• -p, --pretty — column-aligned output for readability

Summarize taxa and loci coverage from a concat provenance TSV. Shows how many loci each taxon appears in, or how many taxa each locus has.

Example:

$ cladekit coverage -t prov.tsv
taxa	loci_present	loci_missing	pct_missing
Mus_musculus	5/5	0/5	0.0%
Smilodon_populator	2/5	3/5	60.0%

$ cladekit coverage -l -p prov.tsv
loci          appearance_count  missing_pct
12S_aln.fas   6/8               25.0%
COX1_aln.fas  6/8               25.0%

Flags:

• -t, --taxa — show per-taxon coverage (how many loci each taxon has)
• -l, --loci — show per-loci coverage (how many taxa each locus has)
• -p, --pretty — column-aligned output for readability

Convert between common sequence data file types. Auto-detects the input format from file contents.

Supported formats:

• FASTA (f)
• NEXUS (n / nex / nexus)
• Relaxed PHYLIP (rp / phylip)
• Strict PHYLIP (sp)

Example:

$ cladekit convert -o n alignment.fasta
#NEXUS
BEGIN DATA;
  DIMENSIONS NTAX=3 NCHAR=8;
  FORMAT DATATYPE=DNA MISSING=N GAP=-;
  MATRIX
  Taxon_A    ATCGATCG
  Taxon_B    ATCGATCG
  Taxon_C    ATCGNNNN
;
END;

$ cladekit convert -o rp alignment.nex
3 8
Taxon_A    ATCGATCG
Taxon_B    ATCGATCG
Taxon_C    ATCGNNNN

Flags:

• -o, --output_format — output format: f (fasta), n (nexus), rp (relaxed phylip), sp (strict phylip)

• filter — remove taxa exceeding a missingness threshold from a supermatrix
• scrub — alignment outlier detection via pairwise p-distances
• view - in terminal alignment viewer
• slice - cut out and remove sections of an alignment (remove non-homologous seqs, extract homologous seqs)

Cladekit is being built as both a real research tool and a vehicle for learning Rust. 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