User: microbeatic

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microbeatic80
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80
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Location:
hanover, NH
Last seen:
3 years, 5 months ago
Joined:
5 years, 9 months ago
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m**********@gmail.com

I answer evolutionary and ecological questions using python, R, and present in Latex.

Posts by microbeatic

<prev • 33 results • page 1 of 4 • next >
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Comment: C: PAML input file format
... FYI: "'cleandata' option is set to 1 in the .ctl file (which is the default)" - actually the default is cleandata=0 (see PAML doc, page 25) ...
written 3.5 years ago by microbeatic80
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Comment: C: How To Install A Specific Cdf Package For Use In Bioconductor
... i was trying to add this to comment instead #quickfingers. ...
written 4.6 years ago by microbeatic80
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Comment: A: How To Install A Specific Cdf Package For Use In Bioconductor
... I think one more bioconductor package that also needs to be installed is `s4vector` http://www.bioconductor.org/packages/release/bioc/html/S4Vectors.html ...
written 4.6 years ago by microbeatic80
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Comment: C: How to keep track of alignment positions after profile alignments?
... Its fasta format. I have been comparing column abundance before and after the alignment, but running into troubles to resolve one to many similarities. Removing gap should work, but my original alignment may contain all gap columns too. ...
written 5.1 years ago by microbeatic80
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How to keep track of alignment positions after profile alignments?
... Hello, Is there a program/way that will keep track of the positions of column before and after profile alignments? For example, muscle does profile alignment fine, but doesnt output which column from alignment 1 was aligned to which column in alignment 2. Thanks ...
profile alignment muscle written 5.1 years ago by microbeatic80
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Does Ncbitblastncommandline Reads The Outfmt (Options 6, 7, And 10 ) Correctly?
... I am trying to call tblastn_hits = NcbitblastnCommandline(cmd='tblastn', query=query_handle, db=db_handle, num_threads=6, evalue=0.001 ...
biopython blast written 5.3 years ago by microbeatic80 • updated 5.3 years ago by Peter5.8k
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Comment: C: Is There A Way To Calculate If Two Columns In Alignment Are Significantly Differ
... I added further explanation. Hope its clear. ...
written 5.4 years ago by microbeatic80
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Is There A Way To Calculate If Two Columns In Alignment Are Significantly Different?
... Given two multiple sequence alignment that have columns that correspond to each other, is there a way to calculate if the two corresponding columns are significantly different? I am trying to distinguish between two closely related groups of homologs. I wanted to identify column/regions between two ...
alignment written 5.4 years ago by microbeatic80 • updated 5.4 years ago by Ashutosh Pandey11k
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How Can I Create A Heat Map With Phylogeny In R?
... I am trying to create a heat map of presence and absence of set of genes in number of organisms. I am using pheatmap, which i think is a fabulous package, if i just want a heat map. But, it doesn't have any options to integrate phylogenetic information. Likewise, i looked into some other R packages ...
R heatmap written 5.5 years ago by microbeatic80 • updated 3.9 years ago by ofanoyi110
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Removing Gapped Columns From A Multiple Sequence Alignment.
... Hello, I was wondering if there is a way in Biopython to remove columns from multiple sequence alignment that have gaps. There is a whole section here on manipulating alignments but there is no function that deals with gaps. My intentions are to remove columns that have gaps of any size, one or a ...
alignment biopython written 5.5 years ago by microbeatic80 • updated 18 months ago by Prakki Rama2.3k

Latest awards to microbeatic

Popular Question 4.6 years ago, created a question with more than 1,000 views. For Removing Gapped Columns From A Multiple Sequence Alignment.
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Does Ncbitblastncommandline Reads The Outfmt (Options 6, 7, And 10 ) Correctly?
Popular Question 4.6 years ago, created a question with more than 1,000 views. For How To Extract Rrna Sequences (In Fasta Format) From Genbank (Bacterial Genome)?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For How To Extract Rrna Sequences (In Fasta Format) From Genbank (Bacterial Genome)?
Autobiographer 5.3 years ago, has more than 80 characters in the information field of the user's profile.

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