RAxML

Podeu descarregar el software de RAxML de la següent adeça: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm

1) Projects - Name a project 2) File administration - Upload an alignment (ex 500.phy) 3) Submit Job - Select file; Application - raxml@titan 4) Topology tree Parameter selection - Evolution Model GTRMIX Number of rate categories to calculate 25 Use random starting tree v rapid hill climbing v Number of alternative runs on distinct starting trees 1000 5) Bootstrap tree Parameter selection - Evolution Model GTRMIX  Number of rate categories to calculate 25  Random number seed (to reproduce a single-CPU job) 5674  Use random starting tree v rapid hill climbing v  Optimize bootstrapped trees v  Number of alternative runs on distinct starting trees 1000  6) In Job Administration, clic to the work required and download a zip file. For the topography, it contains de 1000 trees. At the end of one file (RAxML_info.IND500) it says "Best Likelihood in run number 60: likelihood -46738.453046". The the tree "60" is the best one. 7) Make consensus tree from the bootstrap analysis In Job Administration, clic to the work required and download a zip file.  Open file RAxML_bootstrap.project (has 1000 trees) with FigTree and save as nexus  FIle/Export Trees/ Nexus/Save as currently ...-Save all trees.   Remove commmas ('). Named as bootstrap.t  Go to the folder with the sequecnes in nexus and the tress in nexus. Open MrBayes  exe 500.nex  sumt filename=bootrap nruns=1 ntrees=1 contype=allcompat burnin=0  Use the bootstrap.con  Make two trees  Topology tree. It is a single ML tree but done 1000 different times. Each one can be slightly different and ther is a way to select the "best" one.  Bootstrap tree. Several trees (typically 1000 replicates) are done by recombining the sequence positions at random. It gives a single tree (normally without branch lenghts) with bootstrap values, which have to be added to the topology tree by hand. 1. Open x and go the program folder 2. Copy file with sequences (phylip format) to the same folder 3. Type: ./raxmlHPC -m GTRMIX -n test -s 500.phy -m Which model? GTRMixi It does a fast GTR (a simulation) and ends with a real GTR+G+I -n name of the tree -s name of the input file Name of the file with the tree: RAxML_result.test
 * 1. BioPortal Oslo **
 * 2. How to work with RAxML in a mac computer **