RAxML

→ Install 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