20 months ago
You must follow these steps:
- Align your sequences: you can easily do this with MAFFT online.
- Edit your alignment: you can do this with Gblocks.
- Evaluate the best substitution model
- Run your phylogeny.
You must be very careful in each step, have several methods of alignments with different strategies, you can read the help of MAFFT to set correctly each parameter.
Gblocks by default is extremely strict if your alignment has several non-conserved positions the Gblocks will remove then, you can "flexibilize" the Gblocks edition, changing the block parameters.
The substitution model can be evaluated by Jmodel (for nucleotides) or ProtTest (for amino acids), or you can use the SMS tool in the ATCGPhyML platform (online).
At least, read about the different phylogeny methods (UPGMA, Maximum Parsimony, Maximum Likelihood and Bayesian), think which method is the best for your analysis, and how you can perform your phylogeny in the right manner.
If you use a Bayesian approach, you can use Mr.Bayes or BEAST.
If you use a Maximum Likelihood approach, you can use the PhyML (present in the online version or SeaView platform for Linux) or the RaxML tool (it's a good choice if you are working with genes from polyprotein, because you can set different substitutions model by region of your sequence).
I hope that it can help u.