# 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 NAMEcore_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 RAxML_bestTree.NAME_bootstrap - best-scoring ML treeRAxML_bipartitions.NAME_bootstrap - best-scoring ML tree with support valuesRAxML_bipartitionsBranchLabels.NAME_bootstrap - best-scoring ML tree with support values as branch labelsRAxML_bootstrap.NAME_bootstrap - all bootstrapped treesRAxML_info.NAME_bootstrap - program info# view tree
open
RAxML_bestTree.NAME_bootstrap with → ForesterraxmlHPC -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 treesIn 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 bootstrappingCAUTION: 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 |