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.