NGPhylogeny.fr

Workflow skeleton

Input data

Fasta format

Multiple Alignment

Clustal Omega

Multiple sequence alignment software

Alignment Curation

BMGE

cleaning aligned sequences

Tree Inference

PhyML+SMS

Maximum likelihood-based inference of phylogenetic trees with Smart Model Selection

Tree Rendering

Newick Display

Display a phylogenetic tree as SVG

Configure your workflow

Input data

Choose a file or Paste content
(Fasta format with more than 3 sequences)

Blast runs Files in session

Sequence type

Dealign input sequences

If given already aligned sequences, by default Clustal Omega use the existing alignment to guide creation of the new alignment, by constructing a HMM from the existing alignment. Check this box to realign aligned sequences from scratch.

Clustering guide-tree

By default, only a fraction of the distance matrix is calculated, for speed. Calculate full matrix may be more accurate under some circumstances but is slower and needs more memory.

Use iteration

Redo the alignment multiple times to improve accuracy. Both the HMM and the guide tree will be recalculated each time.

Calculate full distance matrix during iteration

Number of iterations (combined guide-tree/HMM)

Different number of guide tree, HMM iterations

Normally, if iteration is specified, a new guide tree and HMM will be calculated for each iteration. Use this option to restrict the number of iterations for either.

Maximum guide tree iterations

Maximum number of HMM iterations

MSA output order

Display tree guide

Alignment Output format

Sequence Coding

matrix

Name of the PAM matrix [ 1-500 ]

matrix

Estimated matrix BLOSUM

matrix

Estimated matrix BLOSUM

Estimated matrix BLOSUM (if protein)

Name of the PAM matrix [ 1-500 ] (if dna)

Estimated matrix BLOSUM (if protein)

Name of the PAM matrix [ 1-500 ] (if dna)

Sliding Windows Size

sliding window size (must be odd; ranges from 1 to alignment length; if set to 1, then entropy-like values are not smoothed; default: 3)

Maximum entropy threshold

Gap Rate cut-off [ 0-1 ]

Minimum Block Size

Data type

Information file

Precompute file containning sequence description (dna or protein)

Statistical criterion to select the model

Tree topology search

NNI (Nearest Neighbor Interchange)

SPR (Subtree Pruning and Regraphing)

Branch support

Number of bootstrap replicates

Must be a positive integer

Number of random starting trees (no effect when NNI selected)

Display scale bar

Unit name scale

Leaf font

Leaf font-size

Branch support

color

font-size

move

Branch length

color

font-size

move

SVG Tree width (px)

Draw a radial tree