EMBOSS explorer

phyml

Heuristic Maximum Likelihood phylogenetic tree from multiple alignment (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Additional section
Method for estimating support of branches
Number of trials for bootstrap
Nucleic acid evolution model
Protein evolution model
Estimate transition/transversion ratio?
Transition/transversion ratio
Use empirical base/amino acid frequencies?
Estimate proportion of invariable sites?
Proportion of invariable sites
Number of substitution rate categories
Estimate gamma distribution parameter?
Gamma distribution parameter
Starting tree
User provided starting tree:
Optimise tree topology?
Optimise branch lengths?
Tree topology search method
Restart tree topology search with randomized trees?
Number of random restarts
Output section
Base name for output files
Store likelihood for individual bases/amino acids?
Open treefile using NJplot (not for WWW interface)?
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.