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PSI-BLAST creates a protein profile of similar proteins (essentially a scoring matrix based on multiple sequence alignments) that are then used for further DB searches. On the nucleotide level this simply does not make much sense, especially for short sequences. For one, there is much less potential variability which is probably worse for non-coding ...


If you have the budget for it, I highly recommend Geneious for topology work. It was a real saver for me on an epi paper last year. Anyway, they allow for testing per-log likelihood without adjusting edge length. If you want to throw up some dummy data somewhere I can throw up an example. I have no connection or stake with the company, just happy with ...

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