User: virus_n00b

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virus_n00b0
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Posts by virus_n00b

<prev • 12 results • page 1 of 2 • next >
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New element for Sequence Alignment
... I have a list of sequences (12527). On this, I perform MAFFT to get the sequence alignment in clustal format. FastTree is used to generate the phylogenetic tree from the clustal format file. Currently, if I encounter a new sequence then the entire procedure is done again to generate the new phylo ...
sequence sequencing written 18 months ago by virus_n00b0 • updated 18 months ago by RamRS22k
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Comment: C: issue with fasttree package
... Since you are unable to replicate the error, I assume there is something wrong on my side. Can you try the following at your end... 1. Use muscle to convert the Input file using muscle -in b1300dc46e02615c56cd762b141547c0.fasta -out b1300dc46e02615c56cd762b141547c0.muscle -clwstrict -maxiter ...
written 18 months ago by virus_n00b0
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Comment: C: issue with fasttree package
... It is a collection of M's and N's with very few M's. In case the output file is not in fasta format, then the issue must be from MUSCLE side. I am sure that my input file is correct because the same file is used to generate the alignment and phylogenetic tree using the web service (https://www.ebi.a ...
written 18 months ago by virus_n00b0
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Comment: C: issue with fasttree package
... Yes. It is fasta. I have passed the following command to MUSCLE muscle -in b1300dc46e02615c56cd762b141547c0.fasta -out b1300dc46e02615c56cd762b141547c0.muscle I have also added the Input and Sequence file generated by MUSCLE. ...
written 18 months ago by virus_n00b0
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issue with fasttree package
... I need to derive the phylogenetic tree for a group of sequences. I am using MUSCLE to perform sequence alignment. The output of MUSCLE is a sequence aligned file which has the following header MUSCLE (3.8) multiple sequence alignment Now to build the tree, I am using FastTree. I pass the follo ...
sequence fasttree muscle written 18 months ago by virus_n00b0
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Comment: C: Looking for phylogenetic python api
... That's exactly what I needed. Muscle scales well for my problem with -maxiters 2. However, I have a issue in the second part you said "Using fasttree for tree building". MUSCLE outputs a alignment file with header MUSCLE Version number and fasttext is throwing an error for this. Is there any workaro ...
written 18 months ago by virus_n00b0
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Comment: C: Looking for phylogenetic python api
... I'm sure there are no empty sequences. On the other hand, my desired output is phylogenetic tree so can you suggest some algorithms which can scale up to even thousands of sequences? ...
written 18 months ago by virus_n00b0
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Looking for phylogenetic python api
... I have a sequence file (in fasta format) which has 12527 sequences and the length of each sequence is 61. I need to construct a phylogeny tree on this sequence. I am using a python package called "biopython" to perform the below steps: 1. Use clustal omega command line tool to generate the alignme ...
alignment sequencing written 18 months ago by virus_n00b0 • updated 18 months ago by jrj.healey12k
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trouble reading output of clustal omega
... I am using clustal omega provided by *(*( for performing MSA. I have given some sequences as input and got output as shown below. CLUSTAL O(1.2.1) multiple sequence alignment variant9 ------------------------------------------------------------ variant7 --------- ...
sequence alignment written 3.0 years ago by virus_n00b0
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(Closed) How to Characterize evolution
... Hi, I have been going through some terms of Genetics and I have difficulty in understanding them. It would be great if someone can answer the following questions and clarify my doubts. 1. How will you characterize evolution (molecular or viral etc.,)? 2. Are there any metrics or some method to d ...
gene genome next-gen written 3.3 years ago by virus_n00b0 • updated 3.3 years ago by 5heikki8.4k

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