Thread: phylogenetic program that can analyze ambiguity codes

systematicists and phylo gurus,

i am looking for a phylogenetics program that can produce a tree using consensus sequences (dna) that have ambiguity codes (IUPAC codes for multiple bases such as R, K, Y, W, and so on). so far, dnapars/fdnapars is the only one i have stumbled across, but i am not very excited about going the parsimony route. anything bayesian, or at the least, ML-related would be ideal.

your help is much appreciated. thanks

Originally Posted by bhikhaari

systematicists and phylo gurus,

i am looking for a phylogenetics program that can produce a tree using consensus sequences (dna) that have ambiguity codes (IUPAC codes for multiple bases such as R, K, Y, W, and so on). so far, dnapars/fdnapars is the only one i have stumbled across, but i am not very excited about going the parsimony route. anything bayesian, or at the least, ML-related would be ideal.

your help is much appreciated. thanks

BEAUTI/BEAST is a good package. Not sure if it analyses DNA (one would think any package would have this functionality) but is solid bayesian package and superior to most other analysis I have seen.

Otheriwise, common tools include geneiuos, clustal (any such) and you might check out phylogeny.fr. as this site always has links that surprise me.

http://www.phylogeny.fr/

best bet:

http://beast.bio.ed.ac.uk/Main_Page