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Mle: Phyml , phylip and raxml

Mle: Phyml , phylip and raxml. Slides available at: http:// db.tt /bs6TozlY. Data. Data obtained from: http ://www.atgc-montpellier.fr/phyml/ datasets.php Trimmed down 5000 alignments to 1 0 alignments: http :// db.tt /pnsG8wgm Trimmed down 5000 alignments to 1 alignment:

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Mle: Phyml , phylip and raxml

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  1. Mle: Phyml, phylip and raxml Slides available at: http://db.tt/bs6TozlY

  2. Data • Data obtained from: • http://www.atgc-montpellier.fr/phyml/datasets.php • Trimmed down 5000 alignments to 10 alignments: • http://db.tt/pnsG8wgm • Trimmed down 5000 alignments to 1 alignment: • http://db.tt/X3sk3WZc

  3. phylip • http://bioweb2.pasteur.fr/phylogeny/intro-en.html • Click “FASTDNAML”. • Click the “upload” tab. Upload the single alignment. Run! • “The model employed allows for unequal expected frequencies of the four nucleotides, for unequal rates of transitions and transversions, and for different (prespecified) rates of change in different categories of sites, and also use of a Hidden Markov model of rates, with the program inferring which sites have which rates. This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites.” • Documentation: • http://evolution.genetics.washington.edu/phylip/doc/dnaml.html

  4. Phyml • http://www.atgc-montpellier.fr/phyml/ • Enter the 10 alignment data set. • Set number of data sets to “10”. • Select HK85. • Enter your email address and run! • Draw the tree: Copy paste one of the newick trees into • http://cgi-www.cs.au.dk/cgi-chili/phyfi/go

  5. raxml • http://phylobench.vital-it.ch/raxml-bb/ • Upload 1 alignment data set. • Run!

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