
Gblocks all_19_org_1045_core_mafft_aligned_concatenated.faa -g=y -b5=a -e=-gbg > org_core_seq.faa-gbg.log
./mafft2stockholm.pl org_core_seq.faa-gbg
quicktree -boot 1000 org_core_seq.faa-gbg.stockholm > org_core_seq_gap.tre
nw_reroot org_core_seq_gap.tre > org_core_seq_gap.reroot.tre
nw_order -c n org_core_seq_gap.reroot.tre > org_core_seq_gap.reroot.order.tre
nw_display -s -v 20 -l 'font-weight:bold'  -b 'visibility:hidden' -i 'font-size:small;fill:blue' -w 800 -W 20 org_core_seq_gap.reroot.order.tre > org_core_seq_gap.reroot.order.svg
