Subject: Re: Converting newick to nexus
Date: Tuesday 17th September 2013 20:21:41 UTC (over 3 years ago)
Dear Jason, Unfortunately, this issue is perhaps a bit more complicated than just omitting the nexus header ('#NEXUS') after the first tree is printed. As soungalo pointed out, both the header AND the translation table is repeated for every tree. This makes the output file larger than (perhaps) necessary. Optimally (and I think this is what soungalo wanted), the output should contain only a single translation table, and all trees should be written to the same tree block (cf. the output from phylogenetic MCMC software MrBayes, PhyloBayes, etc). This is only possible if all trees contain the same tip labels. Hence, all trees needs to be checked before the trees can be printed in a single tree block. As implemented now, each translation table is created by parsing the order of tip labels in each individual tree. This makes sense if the trees might differ in size and/or labels. But again, if we have many thousands of trees with the same set of tip labels, repeating the translation table should be avoided. I know that an efficient and "optimal" (see above) nexus tree writer is wanted by many, but I'm unsure how much effort that is involved in order to handle the multi tree issue. Yours Johan -- View this message in context: http://bioperl.996286.n3.nabble.com/Converting-newick-to-nexus-tp17013p17153.html Sent from the Bioperl-L mailing list archive at Nabble.com.