User: a.alsayed.phd

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Posts by a.alsayed.phd

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Comment: A: What is the best bootstrap replicates I can use?
... Generally, what are factors determine the bootstrap replicates number that I have to us? can I use 100 or 200 instead of 1000? I have alignments of short seguences length (i.e 200 to 400) from Sanger sequencing of viral-samples ...
written 9 months ago by a.alsayed.phd10
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What is the best bootstrap replicates I can use?
... If I have a couple of (viral) multiple sequences alignments with 200 to 400 nucleotides long, can I use bootstrap replicates of 100 or 300 or 500 instead of 1000? Please, what are the advantages/disadvantages for using less than 1000? ...
sequence phylogenetic tree bootstrap written 9 months ago by a.alsayed.phd10
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Recombination detection tutorial
... Please, can anyone help in step-by-step tutorial on how to assess if there is any recombination events in virus if I have Sanger sequences, MSA., phylogenetic tree, etc? Many Thanks in advance ...
sequencing recombination virus written 9 months ago by a.alsayed.phd10 • updated 12 weeks ago by babin.yurii0
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Comment: C: Bootstrap & p distance distribution
... Many thanks Prof. Kevin for these information ...
written 9 months ago by a.alsayed.phd10
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Bootstrap & p distance distribution
... Dear all, Please, if I have multiple sequence alignments for parts of a virus genome; how can I end up with phylogenetic tree (circular tree) showing bootstrap & p distance on it? Also how can I plot the p distance distribution? Many Thanks in advance ...
phylogenetic tree msa sequencing written 9 months ago by a.alsayed.phd10 • updated 9 months ago by Kevin Blighe26k
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Comment: C: species relative abundance
... Thank you for your advise I know, but I have around 137 rows, 3 examples (OTU ID) as following: k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Micrococcaceae;g__Rothia k__Bacteria;p__ ...
written 11 months ago by a.alsayed.phd10
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Comment: C: species relative abundance
... Thank you for your reply I laready know the abundance for each OTU and I am trying to know the relative abundance and plot it. ...
written 11 months ago by a.alsayed.phd10
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species relative abundance
... Hello, I have OTUs (from 16 s microbiome analysis - MIseq) on excel sheets for many samples. I would like to plot the relative abundance of each species in a graph. I am new to this field, so please, can anyone advise me how to do that? Many Thanks ...
16s written 11 months ago by a.alsayed.phd10 • updated 11 months ago by Brian Bushnell15k
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Answer: A: reference genome alignment
... MSA using DNASTAR lasergene software is one option ...
written 11 months ago by a.alsayed.phd10
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Comment: C: sense versus antisense (plus or minus) sequence alignment
... DNA seqs reads - sanger sequencing of PCR products viral capsid regions (VPs) of human rhinoviruses ...
written 11 months ago by a.alsayed.phd10

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