Automate tronko

[max-mapper]

So far what we know is we need to install/ compile: ancestralclust, famsa, fasta2phyml.pl, raxml, newick_utils, and tronko_build

taxid2taxonpath.py -d nodes.dmp -m names.dmp -e merged.dmp -l delnodes.dmp -i rbcL.fa.taxid -o rbcL.tax.tsv -c 2 -r 1
ancestralclust -i rbcL.fa -t rbcL.tax.tsv -d rbcL_clust -f -r 100 -b 5 -c 4
famsa 1.fasta 1_MSA.fasta 
sed -i ':a; $!N; /^>/!s/\n\([^>]\)/\1/; ta; P; D' 1_MSA.fasta
./fasta2phyml.pl rbcL_clust/1_MSA.fasta 
raxmlHPC silent -m GTRGAMMA -w /home/max/src/cruxcontainer/longest/rbcL_clust -n 1 -p 1234 -T 1 -s 1_MSA.phymlAln
nw_reroot RAxML_bestTree.1 > 1.reroot
tronko_build ...
fast_placer ...