User: Moses

gravatar for Moses
Moses120
Reputation:
120
Status:
Trusted
Location:
united states/ Bloomingtion/ Indiana University Bloomington
Last seen:
5 months, 1 week ago
Joined:
5 years, 11 months ago
Email:
m****************@gmail.com

Posts by Moses

<prev • 73 results • page 1 of 8 • next >
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Comment: C: FastTree error while constructing tree
... UPDATES! : I get the same error after using trimAL software to post-process the alignment ...
written 8 months ago by Moses120
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Comment: C: FastTree error while constructing tree
... yes I want to keep species as much as possible I am interested in strain level differences as well that is the main reason. I am working on reducing the 90k column alignment, and using those 3 criteria it's reduced to 30k. But I will try and refine the alignment using that software you recommended. ...
written 8 months ago by Moses120
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Comment: C: FastTree error while constructing tree
... thank you for your suggestion. I don't understand it however since after manipulation every row has the same number of columns and hence it is a standard MSA file, what is the actual reason for it breaking the program? ...
written 8 months ago by Moses120
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FastTree error while constructing tree
... Hey All, I am trying to infer a phylogeny from a multiple sequence alignment using FastTree program, however the program is giving me an error when I run it over the multiple sequence alignment and I can not figure out what the error is saying (not really that informative). My original alignment h ...
phylogeny multiple sequence alignment fasttree written 8 months ago by Moses120
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Comment: C: pfam tigrfam mixed database
... thank you for your answer! ...
written 8 months ago by Moses120
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pfam tigrfam mixed database
... Hi All, this might be a simple question however I could not find any answers after googling, reading some documentations and descriptions. Basically I have around a 100 tigram domains and then I augmented some domains that were not found in tigrfam database from pfam DB such as Ribosomal S9 domain ...
hmmpress pfam tigrfam hmmer written 8 months ago by Moses120 • updated 8 months ago by Mensur Dlakic6.0k
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Comment: C: RAxML protein partition files
... okay yes that did the trick. I should read this manual more carefully. Thank you for your time and answer! ...
written 8 months ago by Moses120
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RAxML protein partition files
... Hi All, Im using the supermat function in R to generate a super matrix (i.e. concatenate the multiple sequence alignments) and run RAxML over the concatenated MSA file, to do that supermat function is also producing the partitions files. when input the partition file to run RAxML using the -q param ...
phylogeny partition files raxml written 8 months ago by Moses120 • updated 8 months ago by h.mon30k
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Answer: A: running RAxML and MrBayes over concatinated multiple sequence alignments
... After trying many script to concatinate sequences and come up with paritions file for RAxML, catsequences https://github.com/ChrisCreevey/catsequences[catsequences][1] seem to be working [1]: https://github.com/ChrisCreevey/catsequences ...
written 8 months ago by Moses120
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Comment: C: running RAxML and MrBayes over concatinated multiple sequence alignments
... this BeforePhylo script seems to be broken, the output files are messed up and not compatible with RAxML even after specifying the concatination and the partition file to be RAxML format, instead I used the catsequences program and seems to be working so far .https://github.com/ChrisCreevey/catsequ ...
written 8 months ago by Moses120

Latest awards to Moses

Popular Question 6 months ago, created a question with more than 1,000 views. For Maping reactome number to pubmed ID
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Popular Question 15 months ago, created a question with more than 1,000 views. For running CD-hit from python scripts
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Great Question 4.1 years ago, created a question with more than 5,000 views. For running modeller through python scripts
Popular Question 4.1 years ago, created a question with more than 1,000 views. For running CD-hit from python scripts
Popular Question 4.1 years ago, created a question with more than 1,000 views. For FASTA and PIR formats in python
Popular Question 4.1 years ago, created a question with more than 1,000 views. For get the uniprot accession from ensembl protein ID
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Popular Question 4.9 years ago, created a question with more than 1,000 views. For running modeller through python scripts

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