User: Louis

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Louis50
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Posts by Louis

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Sed Remove Boostraps From Mrbayes Trees
... Andreas, your script did not work on my Mac and I'm not certain why. Regardless, thank you for the reply. Arun, your script did the trick. I also found an additional possibility (shown below) that does the same. sed -e 's/:[^,)]*//g' ...
written 7.3 years ago by Louis50
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Sed Remove Boostraps From Mrbayes Trees
... Hello again Biostars, I have what should be a simple sed question but I'm having some difficulty. Please take a look and let me know if you have a solution. I'm trying to use sed to remove bootstrap values from a nexus tree file which was created in MrBayes. Apparently, the newest version of MrB ...
written 7.3 years ago by Louis50 • updated 7.3 years ago by Andreas2.4k
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Comment: C: How To Convert Raxml Bootstrap Format To Phylonet Bootstrap Format
... Thank you Christina! I'll try it and let you know how it works out. ...
written 7.4 years ago by Louis50
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How To Convert Raxml Bootstrap Format To Phylonet Bootstrap Format
... I'm attempting to pipe RAxML trees into PhyloNet; however, PhyloNet's input tree format differs from the RAxML output format. For instance, RAxML reads (... , ...)A:B where A is the bootstrap value and B is the branch length. PhyloNet expects (... , ...)B:A. Thus, I need to switch the position of ...
written 7.4 years ago by Louis50 • updated 7.4 years ago by christina.bergey0
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Answer: A: Error When Piping Raxml Bootstrap Tree File Into Phylonet
... From the developers of PhyloNet: I looked at your file. The gene trees are not in the right format of what PhyloNet accepts. Your format has (... , ...)A:B for internal nodes where A is the bootstrap value and B is the branch length. PhyloNet interprets it as A is the name of that internal node and ...
written 7.4 years ago by Louis50
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Comment: C: Error When Piping Raxml Bootstrap Tree File Into Phylonet
... From the developers of PhyloNet: I looked at your file. The gene trees are not in the right format of what PhyloNet accepts. Your format has (... , ...)A:B for internal nodes where A is the bootstrap value and B is the branch length. PhyloNet interprets it as A is the name of that internal node an ...
written 7.4 years ago by Louis50
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Error When Piping Raxml Bootstrap Tree File Into Phylonet
... I've run into an error when attempting to pipe raxml trees into phylonet. I can successfully use phylonet to construct inferred species trees based on many raxml bestTrees files which have been catenated together as one tree file. However, when I try to pass the catenated bootstrap trees (i.e., bip ...
written 7.4 years ago by Louis50
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Answer: A: Loop Thousands Of Orthologous Msas Into Raxml
... OK - I've found an answer. A friend who knows much more about phylogenetics than I and who has been through this previously, provided direction to make it happen. In summary, you create a working directory containing a subdirectory for each MSA. You can then use a combination of 2 loop.sh scripts ...
written 7.7 years ago by Louis50
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Comment: C: Loop Thousands Of Orthologous Msas Into Raxml
... My bacteria are especially adept at lateral gene transfer so you're correct that not every strain matched locus for locus. It would be nice to retain as much data as possible in the tree. ...
written 7.7 years ago by Louis50
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Comment: C: Loop Thousands Of Orthologous Msas Into Raxml
... Thank you for the reply. I think concatenating the sequences would produce an accurate tree and I will do that; however, a few recent publications are big on using many trees to create a consensus tree and I wanted to try it out as well. I do not know how much they will vary. I'll continue postin ...
written 7.7 years ago by Louis50

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