# Documentation
http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html
# Create tree from → multiple alignment sequences
raxmlHPC -m GTRGAMMA -p 12345 -s alignment.aln -n NAME
# Run RAxML in bootstrap mode
raxmlHPC -m GTRGAMMA -p 12345 -s alignment.aln -n NAME_bootstrap -f a -x 12345 -N 100 -T 12
# Results
RAxML_bestTree.NAME_bootstrap best-scoring ML tree
RAxML_bipartitions.NAME_bootstrap best-scoring ML tree with support values
RAxML_bipartitionsBranchLabels.NAME_bootstrap best-scoring ML tree with support values as branch labels
RAxML_bootstrap.NAME_bootstrap all bootstrapped trees
RAxML_info.NAME_bootstrap program info
# view tree
open RAxML_bestTree.NAME_bootstrap with → Forester
raxmlHPC -help
-p random seed
-s filename of aligned sequences
-n output filename
-T number of threads/CPUs
-f a rapid Bootstrap analysis and search for best-scoring ML tree in one program run
-m GTRGAMMA : GTR + Optimization of substitution rates + GAMMA model of rate
heterogeneity (alpha parameter will be estimated).
With the optional "X" appendix you can specify a ML estimate of base frequencies.
-N 100 Specify the number of alternative runs on distinct starting trees
In combination with the "-b" option, this will invoke a multiple boostrap analysis
-w FULL (!) path to the directory into which RAxML shall write its output files
-x Specify an integer number (random seed) and turn on rapid bootstrapping
CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under
the model of rate heterogeneity you specified via "-m" and not by default under CAT
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