User: Moses

gravatar for Moses
Moses50
Reputation:
50
Status:
Trusted
Location:
united states/ Bloomingtion/ Indiana University Bloomington
Last seen:
1 week, 1 day ago
Joined:
4 years, 6 months ago
Email:
m****************@gmail.com

Posts by Moses

<prev • 42 results • page 1 of 5 • next >
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python equivalent for reorder.dendrogram() R function
... Hi I was wondering if anyone knows any package in python that has the same functionality as reorder.dendrogram() function implemented in R. I just don't want to use R in my code. >https://stat.ethz.ch/R-manual/R-devel/library/stats/html/reorder.dendrogram.html ...
python3 dendogram phylogenetics written 8 days ago by Moses50
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Comment: C: Rooting phylogenetic trees
... is there a python version for this package also? ...
written 8 days ago by Moses50
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Rooting phylogenetic trees
... Hi all, I'm working on a problem where it requires me to have rooted phylogenetics trees such that the tree at any node is strictly bifurcating. I am using FastTree to generate an initial tree. The way FastTree outputs the tree is that the top most node is trifurcating. I tried many ways to reroo ...
python3 phylogenetics tree rooting written 8 days ago by Moses50
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Comment: C: Removing a node from a phylogenetic tree with its edges
... I see. Thanks for that I will check it out. ...
written 8 days ago by Moses50
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Comment: A: Removing a node from a phylogenetic tree with its edges
... For now I'm resorting to tree.prune function that the ete3 package provides. I was hesitant to use this at first because I thought there might (will) be more overhead by getting all the leaves first that I want to keep and then pruning that subtree instead of just removing two nodes from an existing ...
written 9 days ago by Moses50
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Removing a node from a phylogenetic tree with its edges
... Hi All, I have phylogenetic trees with preset outgroups that I am using it to root my trees and convert it to binary trees. I would later want to remove this outgroup with its parent (which is the root for the tree) and continune the tree with the second child of this removed parent which in turn b ...
python3 phylogenetics ete3 written 9 days ago by Moses50
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Comment: C: FastTree trifurcating Root node
... Thank you for your directions. Ill also align it with MAFFT and see what I can get. ...
written 5 weeks ago by Moses50
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Comment: C: FastTree trifurcating Root node
... yes PHYLIP tools are constraining the names, I have to use a different tool since I need those sequence headers to appear fully in the newick file. Concerning for my alignment, what tool should I use to align my sequences since you mentioned above that my alignments dont seem to be optimal? ...
written 5 weeks ago by Moses50
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Comment: C: FastTree trifurcating Root node
... what tool do you suggest to use for alignments? I used MUSCLE to generate that file which I shared the link! Also I'm encountering another problem now that I have noticed: FastTree is not putting my entire sequence names from the fasta headers. For example if in the fasta header from my multiple se ...
written 5 weeks ago by Moses50
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Comment: C: FastTree trifurcating Root node
... update! I tried the Dendropy method, gave the same results as the FastTree program however it takes much more time to execute! ...
written 5 weeks ago by Moses50

Latest awards to Moses

Great Question 2.7 years ago, created a question with more than 5,000 views. For running modeller through python scripts
Popular Question 2.7 years ago, created a question with more than 1,000 views. For running CD-hit from python scripts
Popular Question 2.7 years ago, created a question with more than 1,000 views. For FASTA and PIR formats in python
Popular Question 2.7 years ago, created a question with more than 1,000 views. For get the uniprot accession from ensembl protein ID
Popular Question 2.7 years ago, created a question with more than 1,000 views. For difference between imports in biojava
Popular Question 3.4 years ago, created a question with more than 1,000 views. For running modeller through python scripts

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