For prokaryotes, is 16s rRNA sequencing enough to get a phylogenetic tree?
16S sequences have long been used to infer phylogenetic relationships because they are highly conserved, so I would say that you wouldn't go wrong with them. However, nowadays doing a phylogeny of hundreds of genes is not a problem anymore, so if you have access to more sequences than just 16S, I would definitely use the extra information from these. There was a nice commentary about it by A von Haeseler in BMC Biology last year: http://www.biomedcentral.com/1741-7007/10/13
As for your other question, the guide tree is a perfectly normal phylogenetic tree, but it is used to guide other bioinformatics programs, not to infer specific evolutionary relationships. For example, multiple sequence alignment programs often use a guide tree (which is usually created with a quick phylogenetic method, like NJ) to guide the order of sequences to add to the alignment.
Different regions of the genome evolve diiferently. For example, coding sequences have different mutation rates than non coding sequences. The same happens between genes. Also, different genes (or domains within genes) might have different mutation rates and have higher or lower probably of undergoing a nonsynonymous mutation. Hence, a phylogenetic tree constructed based on one gene is exactly that, one gene tree.
Gene trees might be equal to species trees if you use no paralogs (copies of one gene within one organism), but only true orthologs (copies of one gene in different organisms). However, it is really hard to identify only orthologs because different mutation rates and evolution histories can make paralogs more similar or dissimilar to each other than to their respective orthologs.
So, it depends on what to achieve by constructing a tree based on 16s rRNA. If you want the phylogeny of the 16s rRNA gene, perfect! If you want the approximate phylogeny of the species, not so good although it was used as an approximation by many researchers. However, there are better others to estimate a species phylogeny. You can concatenate several different genes, for example.
16S sequences have long been used to infer phylogenetic relationships because they are highly conserved, so I would say that you wouldn't go wrong with them. However, nowadays doing a phylogeny of hundreds of genes is not a problem anymore, so if you have access to more sequences than just 16S, I would definitely use the extra information from these. There was a nice commentary about it by A von Haeseler in BMC Biology last year: http://www.biomedcentral.com/1741-7007/10/13
As for your other question, the guide tree is a perfectly normal phylogenetic tree, but it is used to guide other bioinformatics programs, not to infer specific evolutionary relationships. For example, multiple sequence alignment programs often use a guide tree (which is usually created with a quick phylogenetic method, like NJ) to guide the order of sequences to add to the alignment.
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