exemplar species has markers for backbone but no markers for clade

naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa

MIT License

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exemplar species has markers for backbone but no markers for clade #40

Closed hettling closed 9 years ago

hettling commented 9 years ago

Using newest supersmart release with order 'primates' as root taxon: Lepilemur jamesi (486960) is exemplar for genus Lepilemur (9452). In the backbone marker table, many markers are listed for this species. However, in the table reporting markers for the clades, no marker for Lepilemur jamesi is listed!

This looks like a bug in smrt BBdecompose and might therefore be related to issue #39.

hettling commented 9 years ago

This was not a bug in BBdecompose, the reason was that the wrong alignment file was used to call BBdecompose (file listing merged clusters instead of file listing all alignments). The workflow for the primate example was there for updated (commit 64642576512329fe5aa1cebfeed095e10b66a40c)