Difference between revisions of "RAxML"
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= Introduction = | = Introduction = | ||
| − | Alexis Stamatakis' phylogenetic tree builder | + | 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 = | = Example usage = | ||
| + | |||
| + | Standard usage | ||
raxml -m GTRGAMMA -s <alignment_of_sequences> -n <chosen_postfix_for_results> -t <sequence_alignment_tree> | raxml -m GTRGAMMA -s <alignment_of_sequences> -n <chosen_postfix_for_results> -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 | ||
Revision as of 11:40, 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 <chosen_postfix_for_results> -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
