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applied-bioinformatics / An-Introduction-To-Applied-Bioinformatics

Interactive lessons in bioinformatics.
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better real-world example of creating tree from biological sequences #11

Open gregcaporaso opened 10 years ago

gregcaporaso commented 10 years ago

The mammal tree based on hemoglobin doesn't work well, I think because the sequences are too similar, but maybe because we need a better distance metric for the aligned sequences that counts using blosum50. Basically want something that has organisms that students can relate to (in that they'll have an intuitive feel for who should be more/less closely related) and that is well annotated so those names are evident.

gregcaporaso commented 10 years ago

This should be possible with 16S, now that SSW makes alignment so much faster.