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Hello,
I am new in this field. I am writing to enquire about a problem that I got while I was following each step of workflow and I am stuck in the step of constructing NJ-tree:
treeNJ
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Dear Dr. Schliep,
I hope this message finds you well.
I am currently using the `phangorn` package to perform a parsimony analysis on a dataset of Clematis sequences. I have encountered an issue…
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Hi! Thanks for the great package, I use parts of it routinely without issue.
I have a question about how to interpret the NAs sometimes outputted in boot.phylo() after using nj(dist(data_matrix)) …
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I stumbled upon 2 bugs when running IQTree v. 1.6.12 for Linux 64-bit on sequences of which some were identical multiple times _without_ the -keep-ident option.
1. Different number of taxa numbers …
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Hi!
Thanks again for developing this tools!
I have successfully ran numbat on many tumor samples, including several large samples (20,000 - 30,000 cell) by reducing the number of cores (thanks f…
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Hi Simon
I hope you can please help with the nan values in the disMat calculation.
I ran the following commands with the .geno data that I prepared with parseVCFs.py. By the way, I have a vcf fil…
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When Expression-Search-NJ 4.0.16 (or 4.0.15) is enabled, it is not possible to open a saved search in a new window. The results windows is blank, and right clicking on the folder pane does not allow …
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It seems that `created` and `modified` do not get set properly when creating a user with the `ticking_creator`. Instead of the frozen time, they get set to the real current time.
I modified the tes…
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Some ideas from a chat with Fred Jaya. Use the wiki to give a few examples of simple benchmarks, e.g.
1. RaxML vs. IQ-TREE on individual loci (fix models to be equal, assess trees in one piece of s…
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I have constructed a ML in R and saved the output as .phy. When I try to open this file in FigTree I get the following message saying the node/branches of the tree are labelled and asking me to select…