PHYLIP to FASTA Converter
Paste a PHYLIP multiple-sequence alignment — sequential or interleaved, strict or relaxed taxon names — and get standard FASTA back. Runs entirely in your browser, nothing is uploaded.
What this tool does
Convert a PHYLIP multiple-sequence alignment into standard FASTA, right in
your browser. Paste the alignment — the count header plus the body — and the tool
works out whether it is sequential or interleaved, whether the taxon names are
strict 10-column or relaxed whitespace-delimited, and writes one >name record
per taxon. Nothing is uploaded: it runs locally, works offline, and needs no
sign-up.
The two PHYLIP layouts
Every PHYLIP file opens with a count header — the number of taxa and the number
of aligned sites, e.g. 3 12. What follows comes in one of two shapes.
| Layout | Body shape |
|---|---|
| Sequential | Each taxon's whole sequence is written out (possibly wrapped over several lines) before the next taxon begins. |
| Interleaved | The first block holds every taxon's name plus the first chunk of its sequence; each later block appends the next chunk, in the same taxon order. |
Taxon names come in two shapes too. Strict PHYLIP puts the name in columns 1–10 and starts the sequence at column 11, with no separator required — which is why classic PHYLIP truncates names at ten characters. Relaxed PHYLIP (the RAxML / PhyML convention) uses the first whitespace-delimited word as the name, so names can be any length.
Leave both selectors on Auto-detect and the tool tries each candidate parse and keeps the one whose sequences match the site count in the header. Force a specific layout or name style when you know your file and want the parse pinned.
Options
| Option | What it does |
|---|---|
| Body layout | Auto-detect (default), Sequential, or Interleaved. |
| Taxon name style | Auto-detect (default), Strict (columns 1–10), or Relaxed (first word). |
| FASTA line width | Wrap each sequence at this many characters. Default 60, the conventional FASTA width; 0 writes one long line per sequence. |
| Uppercase residues | Normalise the sequence case (acgt → ACGT). |
| Strip gaps | Remove the alignment gap characters - and ., turning the aligned FASTA into unaligned sequences. Off by default, so gaps survive untouched. |
| Tolerant | Convert anyway when the file disagrees with its own header — wrong taxon count, wrong sequence length, or unexpected residue characters. Off by default, so mismatches are reported instead. |
Worked example
An interleaved alignment of three taxa over twelve sites:
3 12
Alpha ACGT
Beta ACGA
Gamma TCGA
ACGTACGT
ACGTACGT
ACGTACGT
With FASTA line width set to 0, each taxon's two chunks are joined into one
record:
>Alpha
ACGTACGTACGT
>Beta
ACGAACGTACGT
>Gamma
TCGAACGTACGT
The same alignment written sequentially — Alpha's twelve sites, then Beta's,
then Gamma's — produces exactly the same FASTA, because Auto-detect recognises
both bodies.
Now a gapped alignment with Strip gaps switched on:
2 10
Alpha AC--GTAC-T
Beta ACGTGT--CT
>Alpha
ACGTACT
>Beta
ACGTGTCT
Limits and edge cases
- The first non-blank line must be the count header, two whole numbers such as
3 12. A trailingIorSon that line is read as a layout hint. - By default every taxon's sequence must be exactly as long as the declared site
count, and every residue must be a letter, a digit, or one of
-.?*~. A mismatch names the taxon and reports both numbers; switch on Tolerant to convert regardless. - With Strict name style forced, a name longer than ten characters is cut at
column 10 and the remainder is read as sequence — that is the format's own rule,
not a bug. Use
RelaxedorAuto-detectfor long names. - Interleaved files that repeat the taxon name in every block are handled: the repeated name is detected and dropped rather than pasted into the sequence.
- Gap characters are preserved exactly unless Strip gaps is on, so the alignment columns stay intact for downstream tools.
- FASTA line width is capped at 1000 characters per line.
- Everything runs in the browser tab, so very large alignments are bounded by your device's memory; split huge files before pasting.
FAQ
Do I need to know whether my file is sequential or interleaved?
No. Leave Body layout on Auto-detect and the tool parses the file both ways
and keeps the reading whose sequence lengths match the site count in the header.
Force one of the two only if you want the parse pinned, or if a badly-formed file
is being read the wrong way.
Why did my long taxon names get cut to ten characters?
That happens when the Taxon name style is forced to Strict, where the name
is defined as columns 1–10 of the line. Modern relaxed PHYLIP writers (RAxML,
PhyML) allow longer names separated by whitespace — pick Relaxed, or leave the
selector on Auto-detect, which prefers the relaxed reading whenever it produces
sequences of the declared length.
Are gap characters preserved?
Yes, by default. - and . pass through unchanged, so the FASTA output is still
a valid alignment with the same columns. Turn on Strip gaps when you want
unaligned sequences instead — for example to feed a BLAST search or re-align with
different settings.
What does the site-count error mean?
The header declares how many aligned sites each sequence should have. If a taxon comes out shorter or longer, the file is usually truncated, mis-wrapped, or in a layout that does not match the forced selector. The message names the taxon and gives both the parsed and the declared count, so you can find the offending block. Tolerant converts anyway if you just want the sequences out.
Is my alignment uploaded anywhere?
No. The conversion runs entirely in your browser using WebAssembly. Your sequences never leave your device, and the page keeps working offline once it has loaded.
Developer & Automation Access
Run it from the terminal
Same engine as this page, headless — via the gizza CLI:
gizza tool phylip-to-fasta "3 12
Alpha ACGT
Beta ACGA
Gamma TCGA
ACGTACGT
ACGTACGT
ACGTACGT"New to the CLI? Get gizza →
Open it by URL
Pre-fill and auto-run this tool with query parameters — the names match the API/CLI:
https://gizza.ai/tools/phylip-to-fasta/?phylip=3%2012%0AAlpha%20%20%20%20%20ACGT%0ABeta%20%20%20%20%20%20ACGA%0AGamma%20%20%20%20%20TCGA%0A%0AACGTACGT%0AACGTACGT%0AACGTACGT&layout=auto&name_style=auto&wrap=60&uppercase=true&remove_gaps=true&tolerant=trueMachine-readable descriptor: tool.json — title + parameters JSON Schema for agents.