Sample RAxML Command Blocks

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RAxML allows you to specify the regions of your alignment for which an individual model of nucleotide substitution should be estimated.

This will typically be useful to infer trees for long (in terms of base–pairs) multigene alignments. If, for e.g.,-m GTRGAMMA is used, individual α-shape parameters, GTR-rates, and empirical base frequencies will be estimated and optimized for each partition.

To run multiple model analyses you will need to create a simple text file with a name such as "COI_18Sraxml_part.txt".

If you have a pure DNA alignment with 1,000bp from two genes; gene1 (positions 1–500) and gene2 (positions 501–1,000) the information in the multiple model text file should look as follows:

DNA, gene1 = 1-500
DNA, gene2 = 501-1000

If gene1 is scattered through the alignment, e.g. positions 1–200, and 800–1,000 you specify this with:

DNA, gene1 = 1-200, 800-1000
DNA, gene2 = 201-799

You can also assign distinct models to the codon positions, i.e. if you want a distinct model to be estimated for each codon position in gene1 you can specify:

DNA, gene1codon1 = 1-500\3
DNA, gene1codon2 = 2-500\3
DNA, gene1codon3 = 3-500\3
DNA, gene2 = 501-1000

If you only need a distinct model for the 3rd codon position you can write:

DNA, gene1codon1andcodon2 = 1-500\3, 2-500\3
DNA, gene1codon3 = 3-500/3
DNA, gene2 = 501-1000

For amino acid data you must specify the transition matrices for each partition:

JTT, gene1 = 1-500
WAGF, gene2 = 501-800
WAG, gene3 = 801-800