I strongly recommend you to use MEGA software, and to get a close look at this document link below,

http://mbe.oxfordjournals.org/content/30/5/1229

MEGA can be found on:

http://www.megasoftware.net/

Hope this is useful.

http://www.megasoftware.net/

http://mbe.oxfordjournals.org/content/30/5/1229

In addition to those materials already suggested, I would recommend the book "Phylogenetic Trees Made Easy: A How To Manual", by B. G. Hall, 4th Edition.

http://www.sinauer.com/phylogenetic-trees-made-easy-a-how-to-manual.html

You can try also an excelent introduction to the phylogenetic trees construction hosted at the Howard Hughes Medical Institute: 

http://www.hhmi.org/biointeractive/creating-phylogenetic-trees-dna-sequences

I hope this can help you.

Hi Debarshi.

As mentioned before, the phylogenetic tree can be done by comparing a gene or protein sequence with other sequences deposited in public databases (such as the NR NCBI database). The first thing to do would be the sequencing of a ribosomal gene or other slowly evolving genes/proteins (cytochromes have been used when rRNAs are not sequenced).

Find the closest homologs by blast and make an alignment of the selected sequences. After doing that, consider constructing the tree with a maximum likelihood method and evaluate the statistical reliability of your tree topology with a bayesian method.

If done correctly, the tree can give you valuable information about the evolutionary history of your newly discovered strain, but please be careful enough when assessing the reliability of your tree so any statement you make is supported statistically.

For more info on the subject, I strongly recommend taking a look at the book Molecular Evolution and Phylogenetics by Kumar & Nei, and also to the MEGA software (http://www.megasoftware.net/) and its user manual. The manual also provides many links and references that you may find useful.

Some advice/observations are found here:

https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers?ev=prf_pub

Article Incorporating molecular data in fungal systematics: A guide ...

Hi Debarshi,

I think the trivial work is to find close outgroup to your species. Find the maximum alignment score between your outgroup gene sequence and gene sequences in your species. Then use some MLA such as RAxML to construct your phylogenetic tree. Including bootstrap in your tree will reflect to you how the species are closed to each others.

Hope this can help you.