Fasta File To Phylogenetic Tree
4
2
Entering edit mode
11.4 years ago
Thaman ★ 3.3k

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

fasta phylogenetics • 20k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Maximum likelihood tree

ADD REPLY
5
Entering edit mode
11.4 years ago

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.

ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
4
Entering edit mode
11.4 years ago
Leo Martins ▴ 230

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.

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
4
Entering edit mode
11.4 years ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
ADD REPLY
3
Entering edit mode
11.4 years ago

Mobyle already provides this functionality and more:

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1733 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6