Difference between revisions of "RAxML"
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When using SNPs as input, the following command-line will work: | When using SNPs as input, the following command-line will work: | ||
| − | raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s | + | raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s <snps_as_fasta_file> -p 12345 -n <extension_label_suffixed_to_outputfiles> |
| + | |||
| + | <ins>Explanation</a>: | ||
| + | * ASC refers to ascertainment bias. | ||
Revision as of 13:51, 4 August 2016
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.
