User: samche42
samche42 • 0
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Posts by samche42
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... Hi
I've used a combination of BlastKoala and KEGG to find the presence and absence of genes in three related Burkholderia strains. I used the "Reconstruct Brite" option and 'viewed K00001". The resultant hierarchical list is exactly what I need as the presence/absence of each gene is indicated by ...
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... Hi!
I'm trying to create a single phylogenetic tree from a concatenation of 10 000 individual gene alignments.
I used OMA to find 10 000 orthologous genes from 23 bacterial genomes. I then used muscle to align sequences in multifasta files of each orthologous gene set using the following:
> mu ...
written 3 months ago by
samche42 • 0
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Comment:
C: Clarification of OMA tree metrics
... Thank you!! i really appreciate the help :) ...
written 3 months ago by
samche42 • 0
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... Hi!
I've used OMA 2.2.0 standalone to generate an estimated species tree from 34 genomes. The tree was successfully generated but I can't seem to find any explanations for the numbers on the tree. Are the node numbers the bootstrap values? Levels of similarity? And the scale bar? Is that a reflecti ...
written 3 months ago by
samche42 • 0
• updated
3 months ago by
adrian.altenhoff • 460
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... Hi there
I've successfully uploaded my metadata file and assembled, shotgun metagenomic dataet to my MG-RAST inbox. The metadata passed the QC-like step, my sequwnce data uploaded just fine and I could happily move on to the submission step. Everything works beautifully until I get to the tab where ...
written 14 months ago by
samche42 • 0
• updated
10 months ago by
himanshu.genetics • 0
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