User: apulunuj

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apulunuj0
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Posts by apulunuj

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Comment: C: Filtering gene trees generated by RAXML
... Yes, I generated the trees. But not all the trees are inclusive of the taxa I'm interested in. And there are too many trees to look through by hand. Will the ETE toolkit allow me as you say parse the non-inclusive trees? ...
written 11 days ago by apulunuj0
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Filtering gene trees generated by RAXML
... Hey guys, What is the best way to checking if a set of gene/homolog trees, (about a 1000 tree files), has a certain amount of taxa within them? Baring in mind, you want the trees to also include an outgroup taxon as well. I was thinking about using python along with a dictionary to check for this ...
python raxml R written 13 days ago by apulunuj0 • updated 13 days ago by h.mon15k
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Comment: C: Removing illegal Characters from an Alignment file for RaxML
... Could use this to look at an entire directory as well? @Alex or am I not understanding how to use the sed command? ...
written 9 weeks ago by apulunuj0
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Comment: C: Removing illegal Characters from an Alignment file for RaxML
... Thanks Alex much appreciated ...
written 9 weeks ago by apulunuj0
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Removing illegal Characters from an Alignment file for RaxML
... Hi everyone, I am trying to run raxml on a directory of alignments. Unfortunately, my alignment sequence ID's contain illegal characters( the characters " ; " , " : " and " , "). I figured that I could make a regular expression to match these characters and replace them with an underscore ...
python unix written 9 weeks ago by apulunuj0 • updated 9 weeks ago by Alex Reynolds24k
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Comment: C: OrthoMCL installation on Ubuntu Linux
... Thank you for posting this tutorial. However, I am running into an issue I am not able to compile the makefile. I get this error: make: *** No rule to make target 'Makefile.PL', needed by 'Makefile'. Stop. I made the makefile.pl file as per the instructions. Not sure how to debug the Makefile ...
written 11 weeks ago by apulunuj0 • updated 9 weeks ago by Ram15k
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Comment: C: What is Hit Fraction and how is the Hit fraction determined from blast output
... I was looking for the definition as you explained or pointed out above. Thank you for the references it helped. ...
written 3 months ago by apulunuj0
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What is Hit Fraction and how is the Hit fraction determined from blast output
... Does anyone know any means of checking the hit fraction from a blast output? And what does hit fraction mean particularly? Is this the percentage of sequences that just have the highest score and similarity to the query. Would appreciate clarification and help? ...
blast written 3 months ago by apulunuj0 • updated 3 months ago by h.mon15k
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Comment: C: Unable to install mclust package in rstudio
... Noted thank you. I will take it down. ...
written 5 months ago by apulunuj0
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(Closed) Unable to install mclust package in rstudio
... I am having an issue when installing the "mclust" package on rstudio. I appreciate any and all help with resolving the issue. Here is the warning message:`I am having an issue when installing the "mclust" package on rstudio. Here is the warning message: '>install.packages("mclust") trying URL ...
R linux written 5 months ago by apulunuj0

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