| branch.present | branch.present |
| bsd.dist | bsd.dist |
| bsd.matrix | bsd.matrix |
| clock.space | clock.space |
| collect.clocks | collect.clocks |
| diagnose.clocks | diagnose.clocks |
| gapCR | pathnode |
| get.locus.rates | pathnode |
| get.sptree.rates | pathnode |
| group.clocks | pathnode |
| pathnode | pathnode |
| pca.perm.test | pathnode |
| quart.scores | quart.scores |
| refill.gene.trees | pathnode |
| weigh.clocks | pathnode |
| write.clocks.plots | pathnode |
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