Fasta File To Phylogenetic Tree

Question

[Thaman]

Hi everyone, I am interested in building web application which can take input as a fasta file and then convert those fasta file into an "alignment file" internally. Then i want to build a phylogenetic tree of that alignment tree. Can anyone give a clear guideline to accomplish my project or is this not possible?

Thanks in advance

Thaman

[Ning-Yi Shao]

Your project sounds quite similar to ClustalW webservice: http://www.ebi.ac.uk/Tools/clustalw2/index.html

[Phis]

"build a phylogenetic tree" - what sort of trees would you want to build? Just distance trees, or proper max. parsimony/likelihood or Bayesian inference?

[Thaman]

Maximum likelihood tree

Answer 1

[Khader Shameer]

I have implemented a similar workflow using Fasta file of protein sequence as input, alignment using MALIGN. Output from MALIGN (alignment file) is used as infile for phylip programs

(alignment -> seqboot -> protdist -> neighbor -> consense)

output of distance file is used in modified version of a bioperl script based on TreeIO for the visualization.

If you need any background reading on phylogeny tree implementation, I strongly recommend this article. You can implement this using any combination of programs for example a new improved tool SATCHMO-JS is available for similar application.

[Thaman]

I understood in this way:-

1) Alignment= input (.fasta file ) align (MALIGN, ClustalW) will produce (.aln file) 2) Tree Construction= input (.aln file) implement (NJ, UPGMA) using Phylip, PAUP, clustalw (will produce .tre file) 3) TreeView= input (.tre file) construct (TreeView, JalView)

I am using Python to carry out the project and what else module do i need in python according to listed requirements?

[Thaman]

I succeed in getting Alignment output from MUSCLE. How can i pass command line argument to phylip application suppose i want to use protdist? keeping in mind that phylip doesn't have biopython wrapper. I have been stuck on this problem for atleast 2 days searching command line wrapper for inputting and outputting results between applications.

[Khader Shameer]

You can include phylip in your python script using system command, you can call individual individual programs like protdist, seqboot etc. Remember to provide input parameters in a steering file. For example protdist < pd_input. Here pd_input is a text file with all the parameters that you are planning to pass on to protdist.

[Thaman]

Do i need emboss wrapper to call directly from commandline? Or i can call like "cline=fprotdistCommandline("protdist.exe", input="", output=".tree"

[Khader Shameer]

Posted a detailed answer to your new question : Phylip App'S Without Emboss Tool

Answer 2

[Leo Martins]

Yes, it is possible - and feasible using current programs. You can take a look, for instance, at the DIVEIN and Datamonkey web services. As mentioned by Ning-yi Shao, there are also web servers that do the alignment.

[Thaman]

That means i can use clustalw module in the python? I am just starting in this area and not so clear about uses of tools and algorithms.

Answer 3

[Haibao Tang]

This is certainly possible, and you can get some inspiration from http://www.phylogeny.fr/.

In particular, pay attention to the "a-la-carte" mode (select from Phylogeny Analysis from top menu). A typical phylogenetic reconstruction procedure is a multi-step workflow from making the alignment, improving the alignment, tree building and tree viewing. There are a few choices of programs at different steps - for example, pick a fast alignment method versus a slow but more robust one.

The "one-click" mode exposes less details (and thus less flexibility) for the end-users. With this mode, the application just go ahead with some default programs (MUSCLE,GBLOCKS,PHYML,TREEDYN), that offer reasonable trade-off between speed and accuracy.

[Thaman]

This project is awesome with different features. Wish i can atleast develop some features included in it. Thanks for the description and link. :)

[Thaman]

Clustalw Alignment Problem

Answer 4

[Casey Bergman]

Mobyle already provides this functionality and more:

http://mobyle.pasteur.fr/cgi-bin/portal.py

[Thaman]

I am curious to build my own though i know there are several portal providing same features.