CONDOR: A workflow to detect convergent evolution

Input Alignment Input: sequence file (Fasta format, may be gzipped with .gz extension only).

Input Tree Input: Tree file (Newick format, may be gzipped with .gz extension only).

Outgroup Input: Outgroup file (Txt format, one line per taxon, may be gzipped with .gz extension only).

Phenotype (not used when run mode is "emergence") 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 emergence correlation CONDOR run mode (condor: all analyses, emergence only, or correlation only)

Model Best (IQ-TREE Model finder) POISSON DAYHOFF DCMUT JTT MTREV WAG RTREV CPREV VT BLOSUM62 MTMAM LG MTART MTZOA PMB HIVB HIVW JTTDCMUT FLU MTMET MTVER MTINV Q_PFAM Q_PFAM_GB Q_LG Q_BIRD Q_INSECT Q_MAMMAL Q_PLANT Q_YEAST FLAVI Evolutionary model

Rates No rate heteorogeneity +G4 +G5 +G6 +G8 +G10 +R3 +R4 +R6 +R8 +R10 Rate heteorogeneity among sites

Invariant sites empty +I Invariant sites

Equilibrium frequencies Frequencies of the model Frequencies optimized by maximum likelihood Equilibrium frequencies

Min Seq 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Minimum nb of convergent sequences (≥)

Min EEM 1 2 3 4 5 6 7 8 9 10 11 12 14 16 18 20 Minimum nb EEMs for convergent mutations (≥)

Pvalue Emergence 0.01 0.015 0.025 0.05 0.1 0.15 0.2 Threshold pvalue for emergence

log BF Correlation 2 4 5 7 10 12 15 20 Threshold logBF for Correlation (BayesTraits)

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