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RAxML

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees.
Paste your sequences in the relaxed interleaved Phylip format (this means that the sequence names can be of variable length between 1 up to 100 characters) into the window :

File Pasted

Data example in the relaxed interleaved Phylip format

     


Notification
Email address (required field with bootstrap option; the results will be also sent to you by email)

Substitution Model
Data Type
Substitution model
Algorithm/function you want RAxML to execute (f)
For more details on this methods see the RaxML user manual

Bootstrap
Number of alternative runs on distinct starting trees (N)
Rapid bootstrap random seed (x)
Bootstrap random seed (b)

Others options
User starting tree (t)
Multiple trees file (z)
Weight file name (a)
Number of categories (c)
Start search with a complete random starting tree (d)
Likelihood epsilon (e)
Exclude this file from your analysis (E)
Grouping file name (g)
Print a summary of the program (h)
Initial rearrangement Setting (i)
Write intermediate trees (j)
Optimize branches and model parameters on bootstrap trees (k)
Threshold for sequence similarity clustering (l)
Threshold for sequence similarity clustering (large datasets) (L)
Switch on estimation of individual per-partition branch lengths (M)
Outgroup name(s) (o)
Random number for the parsimony inferences (p)
Protein model (P)
Multiple model filename (q)
Constraint filename (r)
Number of multiple BS per replicate to obtain better ML trees for each replicate (u)


Citation:
Alexandros Stamatakis : “RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models”, Bioinformatics 22(21):2688–2690, 2006 [6].




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Boc, A., Diallo, Alpha B. and Makarenkov, V. (2012), T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks, Nucleic Acids Research, 40(W1), W573-W579.

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Webmasters : Alix Boc and Alpha Boubacar Diallo