Ante Turudic

Calling Tree method t1._diff(t2) causes import error in line: https://github.com/etetoolkit/ete/blob/master/ete3/coretype/tree.py#L1974 I suppose it is not intended to use the method anymore.

Calculation hangs on model with partition

2

Test example contains aligned 56 chloroplast sequences downloaded from NCBI. There are 60 partitions (genes and concatenated inter gene regions). Running that calculations hangs around iteration 6000. Hanging means logging...

I am checking RSCU() method and it seems to me that small performance improvement is possible in codon counting. It should be faster to once call upper() method for a...