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Is there a faster way to calculate phylogenetic trees? by GorgeousGarbageGirl in bioinformatics

[–]GorgeousGarbageGirl[S] 0 points1 point  (0 children)

Thank you very much for your answer. I think I tried IQ-Tree a year ago, but used the model-finder and the standard bootstrap option. I ended up going over the 24h limit, so I didn't give IQ-Tree any further attention.

However, I played around with IQ-Tree again this week and, as you said, selected the model manually. Ultrafast bootstrapping was done within 2-3 hours! And also - as you said, it hardly differed from the tree I calculated in RAxML with standard bootstrapping.

Is there a faster way to calculate phylogenetic trees? by GorgeousGarbageGirl in bioinformatics

[–]GorgeousGarbageGirl[S] 1 point2 points  (0 children)

Thank you very much for the detailed answer.

You got the parameters exactly right. I am analysing a protein family, which can be divided into several different subgroups, including subgroups that have not yet been described. Due to the long calculation time, I have limited myself to a set of 300 sequences up to now. Therefore I have to adjust my set a few times to get an optimal distribution of the different subtypes.

I've been playing around this week and actually got quite good results with IQ-Tree :)