User: microbeatic
microbeatic • 80
- Reputation:
- 80
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- Trusted
- Location:
- hanover, NH
- Last seen:
- 3 years, 5 months ago
- Joined:
- 5 years, 9 months ago
- Email:
- m**********@gmail.com
I answer evolutionary and ecological questions using python, R, and present in Latex.
Posts by microbeatic
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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
microbeatic • 80
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... i was trying to add this to comment instead #quickfingers.
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written 4.6 years ago by
microbeatic • 80
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... I think one more bioconductor package that also needs to be installed is `s4vector` http://www.bioconductor.org/packages/release/bioc/html/S4Vectors.html
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written 4.6 years ago by
microbeatic • 80
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... 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
microbeatic • 80
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... 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
...
written 5.1 years ago by
microbeatic • 80
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8 follow
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... I am trying to call
tblastn_hits = NcbitblastnCommandline(cmd='tblastn',
query=query_handle,
db=db_handle,
num_threads=6,
evalue=0.001 ...
written 5.3 years ago by
microbeatic • 80
• updated
5.3 years ago by
Peter ♦ 5.8k
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... I added further explanation. Hope its clear.
...
written 5.4 years ago by
microbeatic • 80
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... 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 ...
written 5.4 years ago by
microbeatic • 80
• updated
5.4 years ago by
Ashutosh Pandey ♦ 11k
3
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... 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 ...
written 5.5 years ago by
microbeatic • 80
• updated
3.9 years ago by
ofanoyi • 110
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6 follow
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... 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 ...
written 5.5 years ago by
microbeatic • 80
• updated
18 months ago by
Prakki Rama • 2.3k
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 Download Genomes Of All Sequenced Genomes (Draft Or Complete) Within A Phyla From Ncbi Or Jgi?
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
5.0 years ago,
created a question with more than 1,000 views.
For Download Genomes Of All Sequenced Genomes (Draft Or Complete) Within A Phyla From Ncbi Or Jgi?
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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)?
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