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RAxML

# Documentation
http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html

# Create tree from multiple alignment sequences (concatenated core genes)
raxmlHPC -m GTRGAMMA -p 12345 -s core_gene_alignment.aln -n NAME

core_gene_alignment.aln   multiple alignment file from → Roary

# Run RAxML in bootstrap mode
raxmlHPC -m GTRGAMMA -p 12345 -s gene_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



read more

→ RAxML Manual.pdf
→ RAxML Website
→ RAxML Tutorial