Ebi Alignment Tools

Configuration File: ebi_alignment_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the ebi_alignment_tools.json configuration file.

Available Tools

EBI_build_phylogenetic_tree (Type: EBIPhylogenyTool)

Build a phylogenetic tree from a multiple sequence alignment via EMBL-EBI simple_phylogeny. Takes…

EBI_build_phylogenetic_tree tool specification

Tool Information:

  • Name: EBI_build_phylogenetic_tree

  • Type: EBIPhylogenyTool

  • Description: Build a phylogenetic tree from a multiple sequence alignment via EMBL-EBI simple_phylogeny. Takes an ALIGNED FASTA (for example the aligned_fasta output of EBI_msa_align) and returns a Newick tree by neighbour-joining (default) or UPGMA, optionally with Kimura distance correction and gap-column exclusion. Job-based: submits and polls to completion. Use after EBI_msa_align to infer evolutionary relationships among sequences; for raw unaligned sequences, run EBI_msa_align first.

Parameters:

  • aligned_sequences (string) (required) Aligned sequences in FASTA format (>=2 records, equal length with gaps as ‘-‘). Typically the aligned_fasta from EBI_msa_align.

  • clustering (string) (optional) Tree-building method: ‘Neighbour-joining’ (default) or ‘UPGMA’.

  • distance_correction (boolean) (optional) Apply Kimura distance correction for multiple substitutions (recommended for divergent sequences).

  • exclude_gaps (boolean) (optional) Exclude alignment columns containing any gap before computing distances.

Example Usage:

query = {
    "name": "EBI_build_phylogenetic_tree",
    "arguments": {
        "aligned_sequences": "example_value"
    }
}
result = tu.run(query)

EBI_msa_align (Type: EBIMSATool)

Multiple sequence alignment (MSA) of user-provided sequences via EMBL-EBI Job Dispatcher. Unlike …

EBI_msa_align tool specification

Tool Information:

  • Name: EBI_msa_align

  • Type: EBIMSATool

  • Description: Multiple sequence alignment (MSA) of user-provided sequences via EMBL-EBI Job Dispatcher. Unlike pre-computed alignment lookups (Rfam, Ensembl Compara), this aligns YOUR OWN protein/DNA/RNA sequences de novo. Submit >=2 sequences in FASTA, pick an aligner (clustalo [default], muscle, mafft, kalign, tcoffee), and get back the alignment in FASTA and Clustal formats plus a guide tree. Job-based: submits and polls to completion (typically seconds to ~2 min). Use for aligning homologs, building an MSA before phylogenetics, conservation analysis, or designing primers/probes against conserved regions.

Parameters:

  • sequences (string) (required) Two or more sequences in FASTA format (each starting with ‘>’). Example: ‘>seq1nMVLSPADK…n>seq2nMVHLTPEE…’

  • method (string) (optional) Alignment program: ‘clustalo’ (Clustal Omega, default, scales to many sequences), ‘muscle’, ‘mafft’, ‘kalign’, or ‘tcoffee’.

  • sequence_type (string) (optional) Sequence molecule type: ‘protein’ (default), ‘dna’, or ‘rna’. Ignored by muscle (auto-detected).

Example Usage:

query = {
    "name": "EBI_msa_align",
    "arguments": {
        "sequences": "example_value"
    }
}
result = tu.run(query)