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How to improve external node support on a supertree?


Hi All,

I 've run a 4-gene 12,000-taxon super tree. Given I increased the bootstrap repliactes (200 to 1000), the support for the most internal nodes improved a lot (say 80 - 90% BS). However, the support for external nodes are remain low (some of them are 0-10% BS). Regarding to the knowledge that not all the taxa are fully sampled under the 4 genes, so there are great portion of missing data. Well, beside this, any other way to compensate for this shortage?