Matt Moore

Removing dist from internal root node for write

1

Hi! I want to output the internal root node using format_root_node=True but ETE adds the dist (0). So: ``` t = Tree("(A:1,(B:1,(E:1,D:1)Internal_1:0.5)Internal_2:0.5)Root;", format=1) t.write(format=1, format_root_node=True, outfile='outtree.newick') ``` Will output: (A:1,(B:1,(E:1,D:1)Internal_1:0.5)Internal_2:0.5)Root:0;...

With phylo.py, the core genome output doesn't match expectations. Assuming I'm correct in thinking that the .matrix is the right output. With my alignment and a threshold of 0.95, 4,800,000/5,000,000...

Hi Chad, I've coded Panseq so to output locus name and snp position (per the reference) to the end of each row of the snp_table.txt output. With many genomes core_snps.txt...

Is it possible to output query positions

3

Hi, In matches.tsv (python StrobeMap) is it possible to output both reference and query match positions. Thanks and best regards, Matt