User: mdsiddra

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mdsiddra20
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1 month ago
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7 months, 3 weeks ago
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Posts by mdsiddra

<prev • 108 results • page 1 of 11 • next >
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Comment: C: Bootstrap function biopython
... @Eric T. Please have a look here, https://github.com/biopython/biopython/issues/1887 Its urgent. ...
written 5 weeks ago by mdsiddra20
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Problem with getting branch support for phylogenetic tree
... I have used python 3.6 and biopython 1.72 for viewing phylogenetiv trees. I have a protein msa file and a resulting tree file from the data. To evaluate the tree topology, I have generated a 1000 replicate trees for my data. In order to get branch support for my original tree with bootstrap replicat ...
python biopython written 6 weeks ago by mdsiddra20
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Comment: C: Bootstrap function biopython
... Yes, it does. You must post this as question to get complete answer. ...
written 6 weeks ago by mdsiddra20
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Comment: C: Creating text file as a temporary file in python
... Alright, Thanks so much for this help. ...
written 8 weeks ago by mdsiddra20
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Comment: C: Creating text file as a temporary file in python
... Thankyou for the response. Lemme try this with my file if it works. ...
written 8 weeks ago by mdsiddra20
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Creating text file as a temporary file in python
... I have used biopython 1.72 to read from multiple aligned protein data files. I have extracted some required data from the files to other text files which are then used as input to next function. I need to know if I can create that text file to be a temporary file so that as the script ends the file ...
python biopython written 8 weeks ago by mdsiddra20
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Bootstrap function biopython
... I have used bioppython 1.72 modules to generate a Maximum Parsimony tree. I need to know if anyone can help me how to use bootstrap function with biopython.? How can I use this function to evaluate my tree? ...
biopython written 8 weeks ago by mdsiddra20 • updated 6 weeks ago by Eric T.2.3k
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Answer: A: phylogentic tree constuction
... 1) Yes, you may draw your tree without using an outgroup. 2) In any phylogenetic tree, outgroup is the one which is more distantly related group of organisms that can serve as a reference group in order to determine where in the evolutionary history ingroups stand. Now you may understand what effe ...
written 10 weeks ago by mdsiddra20
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Comment: C: Parsimony score of a NJ tree
... As small parsimony problem states that it works with `'n'` number of sequences and an initial tree topology and then uses the heuristic searches (`NNI, SPR,` etc) and calculates the parsimony score resulting the tree with an arrangement of least score. Moreover, as suggested that Neighbor joining is ...
written 11 weeks ago by mdsiddra20
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Comment: C: Parsimony score of a NJ tree
... Lets say we have a particular set of sequences, and a NJ / UPGMA tree for this data too. Can this tree be used as an initial tree topology for parsimony score calculation to result a tree that has minimum evolutionary changes? ...
written 11 weeks ago by mdsiddra20

Latest awards to mdsiddra

Centurion 11 weeks ago, created 100 posts.
Supporter 6 months ago, voted at least 25 times.
Rising Star 6 months ago, created 50 posts within first three months of joining.

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