Hi collegues,
I am trying to get a great tool to despict the phylogeny data but TCS nor Network are useful when ambiguity IUPAC codes are present in the sequences. If someone knows how resolve this problem, I hope you can answer me.
Thanks in advance!
See you!
If you prefer network-like representation I recommend using SplitStree (http://www.splitstree.org/). It is very user friendly and flexible phylogenetic tool. Also I can recommend MEGA (http://www.megasoftware.net/).
Unfortunately haplotype network making programs such as TCS and Network cannot handle ambiguities on the DNA sequences. Moreover, those program are intended for phylogeography studies. In case u really want to make phylogeny inferences, I would like to recommend either Beast or MrBayes. Another alternative is removing the ambiguos sites from your dataset.
The ambiguous nucleotides can be processed in phylogeny by only bayesian analysis using Markov chain Monte Carlo algorithms (MCMC). There are several phylogenetic tools releasing this principle: MrBayes, BEAST, BayesPhylogenies, PhyloBayes, TOPALi etc. If you need another type of analysis (ML, MLk, MP, NJ etc) most likely you'll need to discard your ambiguous sites because there are no way to involve it into current math models of such methods.
Hey, if you are interested in running a ML analyses, RAXML can also read ambiguous code
https://groups.google.com/forum/#!searchin/raxml/ambiguity$20codes|sort:relevance/raxml/RUrN0-F8co8/mp4EwPuPz5QJ
If you need a network instead a phylogenetic inference, then you can PHASE your sequences and then analyse each haplotype independently
http://seqphase.mpg.de/seqphase/
Hope it helps!
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