Use FastTree

Allowed Types: fa, fasta, or a3m
The input multiple sequence alignment you want to use to create the phylogenetic tree. Alignment can be either amino acid, DNA,or RNA sequences. Sequence names must be unique and ensure that they do not contain characters such as ":,()". By default, any text after the first space on a description line will be treated as a comment and will be ignored. For example, the line ">Ecoli arcA protein" is treated as introducing a sequence named "Ecoli". Uneven sequence lengths will result in all sequences getting padded to the length of the longest sequence.

Specify whether your uploaded alignment is for amino acid sequences (proteins) or nucleotides (DNA or RNA).

Choose the substitution model for your uploaded protein alignment. WAG+CAT is optimized for general evolutionary scenarios, while LG+CAT offers enhanced accuracy for diverse and complex datasets.

Use this option to rescale branch lengths and compute a Gamma20-based likelihood. This makes likelihoods more comparable across runs and allows for statistical comparisons of different tree topologies. Note: This increases runtime by approximately 5%.

Use this option to apply pseudocounts, which is recommended for alignments with highly gapped sequences. This helps improve accuracy in scenarios with sparse data.

Optimize for speed and reduced memory usage during the neighbor joining phase. Recommended for alignments with more than 50,000 sequences. Note: This may trade some accuracy for performance.