Input: Query sequences
Input: sequence file (Fasta format, may be gzipped with .gz extension only).
Input: Tree file (Newick format, may be gzipped with .gz extension only).
Input: Outgroup file (Txt format, one line per taxon, may be gzipped with .gz extension only).
Input: Phenotype file (Txt format, sequence names with convergent phenotype, one line per taxon, may be gzipped with .gz extension only).
CONDOR run mode (condor: all analyses, emergence only, or correlation only)
Evolutionary model
Rate heteorogeneity among sites
Invariant sites
Equilibrium frequencies
Minimum nb of convergent sequences
Minimum (strictly) nb EEMs for convergent mutations
Threshold pvalue for emergence
Threshold logBF for Correlation (BayesTraits)
In all cases
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Enter a run name (optionnal) if you would like to remember it more easily.
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