Hi, I have 31 short environmental bacterial 16S reads (250 bp) which remain unclassified at the phylum level, and I want to compare them phylogenetically to a reference set of sequences spanning the whole bacterial domain
I am aware there are two ways to do this: de novo tree building (1) and phylogenetic placement on an existing tree (2) I am also aware of the existence of software such as pplacer, MLTreeMap, EPA, but I am a biology student with no knowledge of programming languages such as Perl, Python, C, or other languages the developed scripts are mostly written in. To make matters worse, I only have Windows to my disposal.
I have been taught to work in Mothur, and the only method I could think of was to align my "john doe" sequences to the Mothur compatible SILVA reference alignment (http://www.mothur.org/wiki/Silva_reference_files) and then calculating a neighbour joining tree by using Clearcut. But knowing that maximum likelihood is better than nj, I'm having trouble sleeping because I wonder whether my neighbour joining tree is reliable.
So next I wanted to submit my multiple sequence alignment to RAxML, but I am unable to convert my fasta file containing 15 000 aligned sequences (file size is 700 MB) to Phylip format. This problem brought me to the following topic: Convert Fasta Alignment To Phylip In Constant Memory, but since I do not know Python, I am unable to use the suggested script.
So my questions to you is:
1) Is there software for phylogenetic placement of short sequence reads that does not require knowledge of programming language or Unix based systems? Or do you suggest de novo tree building instead?
Thanks in advance!