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Proml (PHYLIP)

Paste your protein sequences in the Phylip format into the window (no spaces in the species names; at least one space is required in the end of a species name):
File Pasted

     


User input Tree options
Input sequences interleaved
Search for best tree
Use lengths from user trees
Tree file

Compute options
Speedier but rougher analysis
Global rearrangements
Probability model Jones-Taylor-Thornton Henikoff/Tillier PMB Dayhoff PAM
Outgroup root Outgroup :

Categories and Weights options
One category of sites
Rate for each category (max=9):
Categories file:
Sites weighted
Weights file :

Rate variation options
Rate variation among sites
Coefficient of variation of subtitution rate among sites (1/square root of alpha):
Rate in HMM (including one for invariant if applicable) :
Number of categories
Rate for each category
Probability for each category
Fraction of invariant sites
Rate at adjacent sites correlated ? block length :

Bootstrap options
Analyze multiple data sets Number of sets:
Randomize input order of sequences
Random number seed : Number of times to jumble :

Output Options
Reconstruct Hypothetical sequences


Citation:
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.




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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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