raxml
TLDR
Basic phylogenetic analysis
$ raxml -s [alignment.phy] -n [output_name] -m GTRGAMMA
Rapid bootstrap analysis$ raxml -f a -s [alignment.phy] -n [run] -m GTRGAMMA -x [12345] -N [100]
Parsimony starting tree$ raxml -y -s [alignment.phy] -n [parsimony] -m GTRGAMMA
Multiple threads$ raxmlHPC-PTHREADS -T [4] -s [alignment.phy] -n [run] -m GTRGAMMA
SYNOPSIS
raxml [options] -s alignment -n name
DESCRIPTION
RAxML (Randomized Axelerated Maximum Likelihood) infers phylogenetic trees using maximum likelihood. It's widely used in evolutionary biology for large-scale phylogenetic analyses.
PARAMETERS
-s file
Alignment file (PHYLIP format).-n name
Output file name.-m model
Substitution model.-f algorithm
Algorithm to execute.-x seed
Random seed for bootstrap.-N num
Number of runs/bootstraps.-T threads
Number of threads (PTHREADS version).-p seed
Parsimony random seed.
EXAMPLES
$ # ML search
raxml -s alignment.phy -n result -m GTRGAMMA -p 12345
# Rapid bootstrap + ML search
raxml -f a -s alignment.phy -n boot -m GTRGAMMA -x 12345 -p 12345 -N 100
# Protein sequences
raxml -s proteins.phy -n protein_tree -m PROTGAMMAAUTO
# Partitioned analysis
raxml -s alignment.phy -q partitions.txt -n partitioned -m GTRGAMMA
raxml -s alignment.phy -n result -m GTRGAMMA -p 12345
# Rapid bootstrap + ML search
raxml -f a -s alignment.phy -n boot -m GTRGAMMA -x 12345 -p 12345 -N 100
# Protein sequences
raxml -s proteins.phy -n protein_tree -m PROTGAMMAAUTO
# Partitioned analysis
raxml -s alignment.phy -q partitions.txt -n partitioned -m GTRGAMMA
MODELS
$ GTRGAMMA - GTR + Gamma (DNA)
PROTGAMMAAUTO - Auto-select protein model
GTRCAT - Faster approximation
PROTGAMMAAUTO - Auto-select protein model
GTRCAT - Faster approximation
CAVEATS
Computationally intensive. Use raxmlHPC-PTHREADS or MPI version for large datasets. Superseded by RAxML-NG.
HISTORY
RAxML was developed by Alexandros Stamatakis for high-performance phylogenetic inference, first released in 2004.
