NGPhylogeny.fr

PhyML 3.3_1

Alignment file

phylip/fasta format

interleaved format (if input is phylip)

Interleaved

Data type

Nucleic acids

Amino acids

Auto detect

Evolutionary model

Equilibrium frequencies

Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model:frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.

Transition/transversion ratio

Must be a positive integer, 'e' if you want PhyML to estimate it

Evolutionary model (if DNA data)

Evolutionary model (if Protein data)

Equilibrium frequencies (if DNA data)

Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model:frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.

Equilibrium frequencies (if Protein data)

Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model:frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.

Evolutionary model (if DNA data)

Evolutionary model (if Protein data)

Equilibrium frequencies (if DNA data)

Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model:frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.

Equilibrium frequencies (if Protein data)

Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model:frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.

Evolutionary model

Equilibrium frequencies

Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model:frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.

Proportion of invariant sites

Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter

Number of categories for the discrete gamma model

1 means no gamma model

Parameter of the gamma model

'e' if you want PhyML to estimate it

Tree topology search

NNI (Nearest Neighbor Interchange)

SPR (Subtree Pruning and Regraphing)

Best of NNI and SPR

Optimise parameter

Statistical test for branch support

Use aLRT or aBayes to save computing time.

Number of bootstrap replicates

Must be a positive integer

Seed value used to initiate the random number generator

0 to random seed

User input tree file (optional)

newick format

References to cite