RAxML

Introduction

Alexis Stamatakis' phylogenetic tree builder.

RAxML, like many phylogeny programs is adamant about orthology, and expects to see a high confidence alignment. In practice, this means poor performance with long alignments, and better peformance with gene-level alignments,

Part of this is due to the pitfall of long branch attraction, an phenomenon whereby very dissimilar sequences are grouped together in a phylogeny.

Example usage

Standard usage

raxml -m GTRGAMMA -s <alignment_of_sequences> -n <extension_label_suffixed_to_outputfiles> -t <sequence_alignment_tree>

When using SNPs as input, the following command-line will work:

raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s <snps_as_fasta_file> -p 12345 -n <extension_label_suffixed_to_outputfiles>

Explanation</a>:

• ASC refers to ascertainment bias (known in the original Paul Lewis paper as acquisition bias) accoutn sfor the fact that all the sites are variable, as opposed to other types of alignments which include all the constant or common characters).