User: Elephantdumbo

gravatar for Elephantdumbo
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1 year, 5 months ago
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Posts by Elephantdumbo

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Alternative for phylosim in R
... yea I have done this it worked thanks. I should have came back to add this answer (im terrible at this). Thank you so much for doing that. ...
written 4 days ago by Elephantdumbo20
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Alternative for phylosim in R
... Hey everyone, I want to simulate nucleotide substitution in R and I found this package but it is no longer on CRAN and it is discontinued. This phyloslim ;package https://www.ebi.ac.uk/goldman-srv/phylosim/ Thank you ...
R sequence written 14 days ago by Elephantdumbo20 • updated 6 days ago by maxime.policarpo130
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mutli-character self defined alphabet for multisequence alignement
... Hey everyone, I have seen similar questions asked in the past but no answer. Did anyone figure out how to use multiple sequence alignment with custom multi letter alphabet (4 in this case) with custom scoring matrix. The alphabet will be for example 0001 0200 context: I am tr ...
alignment written 15 days ago by Elephantdumbo20
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Changing distance matrix to scoring matrix to use in alignment software ? (attempt to aligning monomers)
... Hey everyone, I would like to align monemers based on tajima-nei distance. I have already generated the distance matrix and the monemers have the same alphabet as amino acids For example 2 sequences I have would be. >seq1 RAKGKGTGKGKGV >seq2 RKGAKGVNMKG I am trying to use muscle and use ...
alignment sequence written 16 days ago by Elephantdumbo20
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Comment: C: How to get all possible alignments from MAFFT or another global aligner
... Hey Thanks for your response ! I am only interested in pairwise alignment. I will not be aligning 500 sequences. Thanks for the paper. I think it will be helpful I am interested in sub-optimal alignment because I am trying to model repeat clusters misaligning. If you have any advice regarding that ...
written 9 weeks ago by Elephantdumbo20
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How to get all possible alignments from MAFFT or another global aligner
... Hey guys I have two sequences > sequence1 TAGTAGTAG > Sequence2 TAG MAFFT aligns it as TAGTAGTAG ------TAG I want it to also output TAGTAGTAG TAG------ and TAGTAGTAG ---TAG--- Does anyone knows how to do that ? Thank you ...
alignment sequence written 9 weeks ago by Elephantdumbo20 • updated 9 weeks ago by GenoMax93k
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Comment: C: vizulization of the mapping total RNA-seq data to a consensus sequence of a tran
... i used bowtie2 and output bam. should i use salmon or kallisto better ? I think IGV is good ...
written 5 months ago by Elephantdumbo20
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vizulization of the mapping total RNA-seq data to a consensus sequence of a transposable element
... Hello, is there a way i could visualize the mapping of the cDNA to a reference sequence i provide of a transposable element ? I am trying to improve an annotation of a certain element and mapping RNA can help with that because it is a reterotranspon and has an RNA intermediate Thank y ...
transposable elements rna-seq written 5 months ago by Elephantdumbo20 • updated 5 months ago by h.mon31k
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Comment: C: Creating consense tree using bootstrap value support not majority rule
... Yes please. This is exactly what i want ...
written 16 months ago by Elephantdumbo20
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Comment: C: Creating consense tree using bootstrap value support not majority rule
... Thanks your reply. The idea is i am getting different phylip files belong to different reference sequences, but they contain the same samples. I want to infer phylogentic relation ship based on these Philip files. What do you think make sense ? I want to do something the bootstrap thing you sa ...
written 16 months ago by Elephantdumbo20

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