Difference between revisions of "RAxML"
| Line 11: | Line 11: | ||
Standard usage | Standard usage | ||
| − | raxml -m GTRGAMMA -s <alignment_of_sequences> -n < | + | 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: | When using SNPs as input, the following command-line will work: | ||
raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s out_report3.fasta -p 12345 -n OR3 | raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s out_report3.fasta -p 12345 -n OR3 | ||
Revision as of 11:47, 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 out_report3.fasta -p 12345 -n OR3
