Question: Is There Software For Phylogenetic Placement Of Short Sequence Reads That Does Not Require Knowledge Of Programming Language?
gravatar for samlambrechts299
7.7 years ago by
samlambrechts299150 wrote:

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 ( 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!

phylogeny phylogenetics • 4.3k views
ADD COMMENTlink modified 7.4 years ago by Biostar ♦♦ 20 • written 7.7 years ago by samlambrechts299150

try this Molecular Evolutionary Genetics Analysis it is very easy and have example to learn from MEGA it implements Distance, Parsimony and Maximum Composite Likelihood Methods

this also a list of software from Wikipedia if you want to chose another piece of software List of phylogenetics software

also this is a nice book that i recommend for beginners i learned a lot from it Phylogenetic Trees Made Easy: A How To Manual

ADD REPLYlink modified 13 months ago by _r_am32k • written 7.7 years ago by Medhat8.8k

Thank you for your answer! I will have a look at MEGA. In the meantime I also found this: A graphical user Interface for the RAxML Evolutionary Placement Algorithm (EPA; It looks promosing.

ADD REPLYlink written 7.7 years ago by samlambrechts299150
gravatar for cts
7.7 years ago by
cts1.6k wrote:

Are you able to install a virtual machine on your computer that runs linux? If you can't my answer below may not be any use to you, but if you can...

You could use ARB, which contains a GUI for building alignments and trees as well as for insertion of sequences without doing de novo tree building. Databases like SILVA or Greengenes have quite good compatibility with ARB (SILVA is made by the same people who make ARB). It's a pretty archaic looking program, but it's surprisingly feature rich

ADD COMMENTlink written 7.7 years ago by cts1.6k

Thank you for your answer! I have been working with ARB in the lab some time ago, but the resulting phylogenetic placement of my unclassified reads seemed erroneous. This probably was because the alignment produced bu ARB of my reads to the referene sequences was biologically meaningless. I did and do not know how to reliably modify a large alignment in ARB manually, it seems like an impossible job for me

ADD REPLYlink written 7.7 years ago by samlambrechts299150
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