How To Convert Raxml Bootstrap Format To Phylonet Bootstrap Format

Question

[Louis]

I'm attempting to pipe RAxML trees into PhyloNet; however, PhyloNet's input tree format differs from the RAxML output format. For instance, RAxML reads (... , ...)A:B where A is the bootstrap value and B is the branch length. PhyloNet expects (... , ...)B:A. Thus, I need to switch the position of any instance of a integer:decimal combination. Below is an example of a RAxML bootstrapped tree. Has anyone encountered this obstacle previously? Thanks!

(9907:0.00000109805126321607,(MO62:0.17915325940018508866,((((((P466:0.00000109805126321607,AQ4037:0.00000109805126321607)18:0.00000109805126321607,K5030:0.00000109805126321607)12:0.00000109805126321607,RIMD:0.00000109805126321607)14:0.00000109805126321607,AN5034:0.00000109805126321607)78:0.00361692984235871279,((AQ3810:0.00000109805126321607,10329:0.00000109805126321607)24:0.00000109805126321607,9037:0.00000109805126321607)36:0.00000109805126321607)36:0.00000109805126321607,((EX25:0.00000109805126321607,12G01:0.01092837093363076099)98:0.03322610568383993490,(N169:0.30268576131431829124,BA116:0.02960531354461843831)39:0.00877675312720228688)57:0.02111622283920037285)36:0.00362106188593958218)70:0.00000109805126321607,9909:0.00000109805126321607);

Answer 1

[christina.bergey]

Here's a sed command that might accomplish what you want:

sed 's/)\([0-9]*\):\([0-9]*\.[0-9]*\)/)\2:\1/g' < raxml_tree.tre > phylonet_tree.tre

It looks for an ending parenthesis followed by some digits, a colon, and some digits with a decimal point. It then flips the two sets of digits, so your tree becomes:

(9907:0.00000109805126321607,(MO62:0.17915325940018508866,((((((P466:0.00000109805126321607,AQ4037:0.00000109805126321607)0.00000109805126321607:18,K5030:0.00000109805126321607)0.00000109805126321607:12,RIMD:0.00000109805126321607)0.00000109805126321607:14,AN5034:0.00000109805126321607)0.00361692984235871279:78,((AQ3810:0.00000109805126321607,10329:0.00000109805126321607)0.00000109805126321607:24,9037:0.00000109805126321607)0.00000109805126321607:36)0.00000109805126321607:36,((EX25:0.00000109805126321607,12G01:0.01092837093363076099)0.03322610568383993490:98,(N169:0.30268576131431829124,BA116:0.02960531354461843831)0.00877675312720228688:39)0.02111622283920037285:57)0.00362106188593958218:36)0.00000109805126321607:70,9909:0.00000109805126321607);

You should test this out in PhyloNet before relying on it, naturally.

[Louis]

Thank you Christina! I'll try it and let you know how it works out.