Here’s a link to a Master’s thesis on this subject, published in 2011, referencing some relevant literature (PDF download)
http://scholar.sun.ac.za/bitstream/handle/10019.1/19938/botha_evolutionary_2012.pdf?sequence=1
MEGA is easier to use, imho. It is the choice software of all creationists that do phylogenetic analysis. Carter, Jeanson and others use it in their research on Adam and Eve.
I used MEGA for some of my work on Tetrapod evolution and PTM comparisons on TopoIsomerases.
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That says a lot about the professional abilities of creationists. MEGA is a sequence alignment program that will also do very quick and dirty phylogenetic analyses, not suitable for prime time. No phylogeneticists use MEGA for anything other than alignment, and usually not that, as there are better alignment programs. MUSCLE is popular.
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Jeanson seems to simply rely on the “draw tree” button in ClustalX, which produces the most basic NJ or UPGMA tree, then just visualises that tree in MEGA.
Could this be a consequence of not believing that the tree actually exists, and thus isn’t worthy of real effort?
But surely they believe that some trees do exist. Just not a universal tree.
I agree. In my experience, MEGA is the phylogenetic software of choice for scientists who know they need to make a phylogeny but are not very familiar with how phylogenetic inference works and don’t want to have to consult somebody else with more phylogenetic expertise.
He certainly tries to use tree topologies and branch lengths to draw some grand conclusions (e.g. in the link below), so I’d imagine he would want them to be as accurate as possible.
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But he thinks the tree exists only within families, and he uses branch lengths to draw conclusions from a tree that includes whole orders, a tree that he doesn’t believe exists. (I also don’t understand his point about branch lengths, which considering the poor analysis he performed are almost certainly bogus. He appears to have done a simple NJ tree with whatever the default distance measure is, and I would guess that to be just simple matching distances. Given mitochondrial data, the older branches are almost certainly highly compressed due to saturation.)
Absolutely. I talk about it all at length in my blog post about his mtDNA arguments:
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Well, that was a thorough demolition.
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MUSCLE is inside MEGA. I showed MUSCLE alignments to you that I did in MEGA. And doesn’t Nei use MEGA? He’s a professional, ain’t he? 
A good evidence of evolution are the patterns of similarity, particularly conserved features in the lobster brain and the human brain.
Jordan Peterson argued that dominance hierarchies are embedded into animal kingdom, hence the dominance hierarchy that left-wing feminist social justice warriors claim is merely a social construct is totally is not.
So Peterson demolishes left-wing feminist/marxist men-hating post modern social justice warriorism tyrrany in favor of free market capitalism. God bless him. That’s my kind of evolutionary biology!
Here is Peterson taking it to Cathy Newman, the Lobster evidence is toward the end:
[@Moderators removed long and political video with no relevance to post]
I was injecting a bit of humor, but mocking and ridicule of me is permitted here? BYE! I’m out of here.
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Where were you mocked @stcordova. Please flag the post and it will be dealt with, okay? If you really want that video back, we can restore. Seems like a strange place to draw the line.
Dr. Sawmidass,
I don’t mind being mocked or ridiculed, perhaps the way I write and interact isn’t going to go over well here and will not be within the rules, so I prefer to opine elsewhere.
We can always communicate with each other in other venues. Things are cool between us. God bless you. And Happy Thanksgiving and an Early Merry Christmas.
Thank you for all that you are doing for the Christian faith and God’s church.
I like your contributions. I hope you stay. The only post that was edited was for precisely the reason I gave. And I undid the edit at your request.
What exactly is your complaint? I’d love to fix it for you.
Also, to be clear, you have been in the rules. I’m very confused as to what your objection is here.
He’s a professional biologist, but he isn’t a phylogeneticist. Of course, he likes neighbor joining. I wonder why.
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Without some indication that a post in intended to be humor or sarcasm, it’s easy to mistake the intent. Emoticons are your friend! 
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Not if you are John Harshman!
