MSA-tools

MSA Taxon Filter

Filter a multiple sequence alignment (MSA) to keep only sequences from representative eukaryotic species. Upload your MSA file (FASTA or A3M) or paste its content, then choose a species set.

Preset guide: All 643 species = full sparse eukaryotic tree; 262 species = balanced subset of the sparse eukaryotic tree; 50/20/10 species = diverse eukaryotic representatives; Specific clade = choose a clade and the number of representatives from below.

Step 1 — Input MSA

Upload your MSA file (FASTA or A3M)

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Or paste MSA content directly (FASTA or A3M)

Step 2 — Select model species

Species set*

Clade (only if preset = Specific clade)

Number of representatives (only if preset = Specific clade)

Step 3 — Fallback Options

If a sequence's header doesn't contain a clear species identifier (like OX= or an Uniprot ID), you can use a fallback strategy to identify it.

Fallback method for sequences without direct identifier*

Enable common name matching (e.g. 'HUMAN', 'MOUSE') as a last resort

Step 4 — Job name

(Optional) Give your job a name (max 30 characters)

Reset fields