I want to generate phylogenetic tree of my protein sequences by TreeBest software for that I want my sequences in these format (.nhx , .nh or .mfa ) for further analysis right now they are in fasta format . Please suggest some convertor or methodology.
If I'm not mistaken, BioPerl can help you but it will need some coding skills from you. Take a look ate this tutorial page from BioPerl website (http://www.bioperl.org/wiki/HOWTO:Trees). You can save to file your sequences in the New Hampshire format.
Hi Yogesh.
Im not quite sure about your question. The NHX format (at least the format that i known, the New Hampshire eXtended format) contains the information for a phylogenetic tree generated based in a set of aligned protein or dna sequences. Fasta or multifasta format contains a group of sequences.
So in my opinion you cant convert one in other because are two differents type of information.
Perhaps you are try to construct a phylogenic tree based in your alignment. You can try PHYLIP package to read your ultiple alignment and export the tree in NHX or NH format.
Best regards,
Christian.
Dear Yogesh,
as Felipe and Christian already described, sequences are saved in text file in fasta format yielding .fasta files in order to serve as input for multiple sequence alignment. After this step is finished, evolutionary/phylogenetci relationships can be reconstructed using a number of methods (Distance - Neighbor Joining, Maximum PArsimony, Maximum Likelihood, Bayesian ) implemented in programs ranging from PHYLIP 3.6 to MEGA 5.2 or 6 and multiple other. After the most suitable model is selected using AIC or Bayesian Criteria, it can be used to generate the most probable phylogenetic tree that one can export in numerous different formats. For conversion of formats one could simply use TreeView, but there are numerous others.
Best,
Blaz
Thank you all for you explanatory answers.
dear christian my aim is to generate phylogenetic tree from fasta format multiple sequences but i want to use TreeBest tool for phylogenetic tree which support only .NHX, .NH and .MFA format, for that i want to know how should i come to that format.
Hi, I had a look at TreeBest. You still need to first reconstruct a gene tree from your aligned sequences stored in fasta format and compare this tree to the species tree of your organisms.
Have a look at http://treesoft.sourceforge.net/njtree-old.shtml on NJtree which was the starting point for designing TreeBest.
Hi Yogesh,
Now it's more clear.
NHX or NH format already contains the phylogenetic tree, so TreeBest use this files to open, show and analyze the phylogeny. So it's implicit in this that you already generate the philogenetic tree.
On the other hand, the MFA format correspond to a multiple align and, as Blaz mention, your first step to reconstruct the phylogeny is generate this file. MAVID aligner for example (http://bio.math.berkeley.edu/mavid/download/) generate 2 outputs and one of them is the MFA alignment.
Hope this help. Best regards,
Christian
Thank you so much Blaz and christian for these answers they are very help full for me.
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