Phylogenetic analysis tools and bioinformatics pipelines.

3DCoffee / Expresso with validated FASTA inputs, original executable and downloadable scientific outputs.

Species tree inference from a set of gene trees using ASTRAL-IV or ASTRAL-Pro3 (ASTER).

Sequence similarity search using BLAST

BMGE with validated FASTA inputs, original executable and downloadable scientific outputs.

ClipKit with validated FASTA inputs, original executable and downloadable scientific outputs.

Clustal Omega with validated FASTA inputs, original executable and downloadable scientific outputs.

Multiple sequence alignment using the ClustalW 2.1 binary, with FASTA, PHYLIP and CLUSTAL outputs.

Discovery of cis-regulatory long-range elements correlated with gene expression using DExTER.

Estimate branch lengths on a fixed phylogenomic topology and relative evolutionary rates from gene distance matrices.

FastME 2.0: a comprehensive, accurate and fast distance-based phylogeny inference program

FastTree with validated FASTA inputs, original executable and downloadable scientific outputs.

Conserved-block selection from an existing multiple sequence alignment, with normalized FASTA and PHYLIP outputs.

Maximum-likelihood phylogeny inference from an aligned sequence file using IQ-TREE 3, with optional ModelFinder, SH-aLRT and ultrafast bootstrap support.

MAFFT with validated FASTA inputs, original executable and downloadable scientific outputs.

Search for motif occurrences on reference genomes with curated and custom matrices.

Matrix Representation with Parsimony (MRP) supertree inference from two or more Newick trees using PAUP*.

Multiple sequence alignment with MUSCLE 3.8, producing FASTA, CLUSTAL and PHYLIP outputs.

Bayesian phylogeny inference from an aligned FASTA file, with consensus tree and posterior diagnostics.

Neighbor joining with PHYLIP Dnadist/Protdist and optional site bootstrap/Consense. All scientific work runs on the MYST runner.

Maximum-likelihood phylogenetic inference with broad model and optimisation options.

PhySIC_IST supertree inference with optional STC and bootstrap-based correction.

ProbCons with validated FASTA inputs, original executable and downloadable scientific outputs.

Maximum-likelihood phylogeny inference from an aligned sequence file using RAxML-NG, with optional non-parametric bootstrap support.

Sequence format conversion using BioPython, supporting FASTA, PHYLIP, CLUSTAL and other formats.

Explore k-mer conservation in intrinsically disordered protein regions.

Smart Model Selection (SMS) to rank substitution models with optional PhyML inference.

Multiple sequence alignment with T-Coffee, returning aligned FASTA, CLUSTAL, PHYLIP, guide-tree and optional legacy export formats.

TFScope analyses TF binding from positive/negative BED peaks and motif collections to extract discriminative features.

TFscope 2 explains binding differences using discriminative motifs, positional nucleotide environments and co-factor motifs.

Parsimony phylogeny inference from an aligned FASTA file using TNT 1.6, with strict consensus output.

Render a Newick tree as a lightweight SVG preview suitable for web display.