Does this send my sequence anywhere?

Yes, and only when you press run. This is one of the two tools that leave the machine: the sequences are submitted to EMBL-EBI, which is stated in the panel before a run. Every other tool in the workbench stays local.

Why not just use the local aligner?

The local partial-order aligner is the default and needs no network. This exists for when a reviewer expects Clustal Omega or MUSCLE numbers specifically, and for the pairwise statistics EMBOSS reports.

What happens to the tree it returns?

The guide tree is saved as a Newick file in the project, which the phylogenetics tool reads directly.

Analyze

EMBL-EBI Services

The local aligner stays the default. This is for the moment a result has to be defensible: run the same sequences through the aligner the field cites and read both numbers. Sequences come from the project, and what comes back hands off to the tools that consume it.

Open EMBL-EBI Services Open the BLAST & EMBL-EBI services sample

Nucleotide, protein, an annotated plasmid and a headerless raw sequence: reach blastx, blastp and blastn, and every EMBL-EBI service, on real queries

What it does

01Clustal Omega and MUSCLE multiple alignment, with the service percent-identity matrix and its Newick guide tree
02EMBOSS needle (global) and water (local) pairwise alignment, with the service identity, similarity, gaps and score
03HMMER phmmer search, split at the service inclusion threshold
04Phobius signal-peptide and transmembrane topology prediction
05Sequences taken from the project and the current selection, never retyped
06The guide tree saved as a real Newick file for the phylogenetics tool, and the aligned FASTA saved into the project
07Job progress, cancellation on the service, and a history that reopens a past run

What it runs on

One shared client for the EMBL-EBI Job Dispatcher (submit, poll, fetch result), with every parser asserted against captured real jobs. The panel runs on @ports/jobs.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Does this send my sequence anywhere?: Yes, and only when you press run. This is one of the two tools that leave the machine: the sequences are submitted to EMBL-EBI, which is stated in the panel before a run. Every other tool in the workbench stays local.
Why not just use the local aligner?: The local partial-order aligner is the default and needs no network. This exists for when a reviewer expects Clustal Omega or MUSCLE numbers specifically, and for the pairwise statistics EMBOSS reports.
What happens to the tree it returns?: The guide tree is saved as a Newick file in the project, which the phylogenetics tool reads directly.

Also searched as

clustal omega online · MUSCLE alignment online · EMBOSS needle online · EMBOSS water local alignment · phmmer search · phobius transmembrane prediction · EMBL-EBI job dispatcher · Clustal Omega alternative · MAFFT alternative online · Needleman-Wunsch online · Smith-Waterman online · pairwise sequence alignment online · run EMBL-EBI tools from the editor