Phylogenetic Profiling

Domain presence/absence matrix across taxa, and high-resolution phylogenetic profiling.

Domain Presence / Absence

Build a domain presence/absence matrix across taxa. Continue to high-resolution profiling when ready.

Filters

UniProt Version

Pfam Names / Accessions Comma separated. Multiple entries build multi-column matrix.

Taxonomy IDs (comma separated, leave blank for all) Or upload a file (one ID per line)

Apply E-value cutoff

Carries your version, Pfam, and taxonomy selections into the high-resolution step.

High-Resolution Phylogenetic Profiling

Build gene trees, partition them into subclades, and assemble a high-resolution profile.

Filters & Build Trees

Partition Trees

Assemble Profile

Protein Filters

UniProt Version

E-value cutoff (optional)

Pfam IDs / HMM names Comma or newline separated. One tree is built per entry.

External FASTA (optional) Combined with the Pfams above as an extra gene tree. Headers must be {taxid}.{accession}, e.g. >9606.P04637. You can supply Pfams, a FASTA, or both.

Taxonomy

Taxonomy IDs (optional)

Exclude taxonomy IDs (optional)

Tree Build Parameters

Output / cache directory Per-config subdirectories are created here. Repeated runs with identical parameters reuse cached trees.

Aligner

Tree method

trimAl -gt

CPU threads

Building trees…

ETE Species Tree Profile

Standalone — uses NCBI taxonomy

Visualize HMM domain counts directly on the NCBI taxonomy tree using ETE4. Upload your hmmsearch --tblout output, a branch-colour map, and a taxids list.

Input Files

HMMsearch tblout *

Colormap file * Tab-separated: taxid → hex color, one per line.

Taxids file * One NCBI taxid per line.

Options

Max domain count

Database Connection

Phylogenetic Profiling

Domain Presence / Absence

Presence / Absence Matrix

Clustered Heatmap

Co-occurrence results

High-Resolution Phylogenetic Profiling

Tree-Build Summary

Species Tree (NCBI taxonomy)

Profile Assembly

Heatmap

Matrix

View Profile on NCBI Tree (ETE4)

ETE Species Tree Profile