| Protein sequences |
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If not checked, DNA sequences will be assumed |
| Outgroup |
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The name of one or more (comma-separated) outgroup(s) can be specified |
| Substitution matrix |
DAYHOFF
DCMUT
JTT
MTREV
WAG
RTREV
CPREV
VT
BLOSUM62
MTMAM
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| Use empirical base frequencies |
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| Use a mixed/partioned model? |
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You may provide an alignment partition file |
| Per gene branch length optimization |
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| Maximum likelihood search |
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Will search for best-scoring tree after the bootstraps |
| Estimate proportion of invariable sites |
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| Use a multifurcating constraint tree? |
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The name of a file that contains a multifurcating constraint tree. This tree does not have to be comprehensive |
| Automatically determine the number of bootstrapping runs |
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If checked, RAxML will automatically determine the point at which enough bootstrapping replicates have been produced |
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