Looking to ID hypervariable sites and/or regions within the CR of a species of cetacean from a sample size of 150.
In this paper we discuss tools and programs for phylogenetic inference:
https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers
My opinion is that TNT is by far the best program for parsimony analysis. Using it is not entirely trivial though.
Article Incorporating molecular data in fungal systematics: A guide ...
There are quite a few that you could use, I quite like TNT (http://www.lillo.org.ar/phylogeny/tnt/) - though it can be a bit fiddly at first.
Phylip works great for me.
If I may offer a suggestion, parsimony methods have generally been regarded to be less accurate compared to other methods like Maximum Likelihood and Bayesian.
MEGA 6 can reconstruct a Maximum Parsimony tree. You just need a .meg file. You can use MEGA to convert fasta files in mega.
PAUP* is arguably the most-used, most-cited and best-sold program with a wealth of tree search options and algorithms (also beyond parsimony only) and it 's user-friendly in my opinion. Moreover, the NEXUS file format for input is quite universal and usable in other phylogenetic programs. PAUP* can be criticised for example for having so many options that sometimes you can't see the forest through the trees (no pun intended) and that the program is quite expensive. There are some free downloadable programs. If those that others recommended you are free I don't know; I hope others will tell you in this forum.
The others are all free programs, but PAUP is still probably the most widely used and a solid program, you are right Kenneth.
PAUP, MEGA and TNT are programs you can use, but I also prefer PHYLIP.
In this paper we discuss tools and programs for phylogenetic inference:
https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers
My opinion is that TNT is by far the best program for parsimony analysis. Using it is not entirely trivial though.
Article Incorporating molecular data in fungal systematics: A guide ...
As said, PAUP* is the most used for parsimony and with the PAUPRat script you can speed up the tree search a lot using a parsimony ratchet approach.
You can find new test versions for free, even with a GUI for Windows, in the author's webpage (see link below).
http://people.sc.fsu.edu/~dswofford/paup_test/
Article The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
I use MEGA 6 (btw, as distinct from the Mega 5, in this version the conversion of your .fas file into the .meg file is not obligatory) and in the majority of cases it is nicely working.
Btw, is anybody familiar with ARB-parsimony tool? I can not properly import the short sequences into existed tree in ARB. Sorry for off-topic...
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