We are into bacterial community analysis. As stated above we want to draw a phylogenetic tree based on 16S rRNA genes. As we have read in some publications it is possible first to draw a scaffold tree and then integrate the own sequences.

For example in the publication of Fernández and coworkers (Comparison of prokarytoic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach; doi: 10.3389/fcmicb.2014.00196) the tree displayed in figure 7 was  constructed by near full length reference 16S rRNA gene sequences and then the metagenomic reads were added without altering the tree topolgy.

We would like to know, how to elaborate such a tree. Any input or hints are welcomed!

We do have experience with the program package phylip (Felsenstein).