RAxML-NG

Infer maximum-likelihood phylogenetic trees from aligned protein or DNA sequences with bootstrap support.

Job name

Alignment

Configure input settings on the left, then click "Infer Tree"

Related tools

HMMER

Sensitive sequence homology search using profile hidden Markov models. More accurate than BLAST for detecting remote homologs, ideal for finding evolutionarily distant protein family members.

MAFFT

Perform multiple sequence alignment using MAFFT (Multiple Alignment using Fast Fourier Transform). Supports multiple algorithms from fast progressive to highly accurate iterative methods.

MMseqs2

Ultra-fast sequence search and clustering. 10,000x faster than BLAST for database searches, with powerful sequence clustering capabilities for proteins and nucleotides.

MUSCLE5

Perform multiple sequence alignment using MUSCLE5 (MUltiple Sequence Comparison by Log-Expectation). Uses the PPP algorithm for high-quality alignments with support for ensemble generation.

RNAdistance

RNAdistance compares RNA secondary structures using the selected upstream ViennaRNA distance representation and comparison mode.

AF-Cluster

Cluster Multiple Sequence Alignments to predict alternative protein conformations with AlphaFold2. Uses DBSCAN clustering to identify sequence subgroups.