5 votes
Accepted

Construct phylogeny from a Fasta file

You will first need to align your sequences, and then feed the alignment to a program that can generate trees. I am very much out of date in this field and I haven't done anything like that in at ...
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1 vote

Construct phylogeny from a Fasta file

Here's the result from FigTree. I thought there was a bug in the newick file, but it was fine. I strongly recommend the answer by @terdon because there are other issues here, for example ...
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  • 7,339
1 vote
Accepted

Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?

IQTree is a fashionable method for speeding up bootstrapping and used on ultra large datasets. What IQTree might be doing is rigidly fixing a model and parameterisation is not estimate via the ML. ...
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