User: al-ash
al-ash • 100
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Posts by al-ash
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... ...the link is dead and I still get the first line empty after redirecting the output into a file - could you update the answer if there is a more elegant way (not piping through tail) to avoid this? ...
written 3 months ago by
al-ash • 100
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... "ITS (Internal Transcribed Spacer) is part of the non-transcriptional region of the fungal rRNA gene" is a bit misleading (it is like defining DNA as the genetic information carrier of birds - i.e. not incorrect, but...) ...
written 4 months ago by
al-ash • 100
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Comment:
C: SRX from SRR IDs
... Be careful though when converting larger number of accessions. When converting ca 500 Sample accessions to Run accessions, somewhere in the middle of the process, one conversion failed for me with "Can't fetch uids from history because of: Result not ready". ...
written 4 months ago by
al-ash • 100
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... Thanks! https://stackoverflow.com/questions/46626414/how-do-i-generate-all-possible-newick-tree-permutations-for-a-set-of-species-giv/46670077#46670077 is very close - I think I can generate the bifurcating trees by taking this solution and removing the polytomies (which I can do here by e.g. removi ...
written 6 months ago by
al-ash • 100
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... I'd like to generate all existing bifurkating newick trees for a set of N taxa (specifically N=5 for my task but I would prefer a general solution for N).
The tool or code would ideally take as input a set of N strings (e.g. "species1","species2","species3","species4","species5") and generate all p ...
written 6 months ago by
al-ash • 100
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... I think consensus() is not doing what I'm looking for here - to compare a reference tree with a set of some other trees and generate a tree with the same topology as the reference tree but additionally containing conflict/support information accumulated from all the other input trees. ...
written 6 months ago by
al-ash • 100
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... I'd like to combine boostraps/priors from multiple phylogenetic trees onto a reference tree topology. The trees would contain identical set of taxa (tip labels) and distinct node/branch values. In the resulting tree, the node/branch information from the trees should be saved into the reference tree ...
written 6 months ago by
al-ash • 100
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... Please show also the headers of the alignments which "are fine" to see if the problem is header length.
I had this error when my input phylip file had between sequence name and sequence tab instead of two spaces. Replacing the tab by two spaces (e.g. in bash via sed 's/\t/ /') fixed the problem - ...
written 6 months ago by
al-ash • 100
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... Since this is one of the top hits when searching online for manual editing of multiple alignments, I'd like to reopen this topic to hopefully collect suggestions for some more tools than JalView for visual inspection and editing of multiple sequence alignments.
One common task is identification of ...
written 7 months ago by
al-ash • 100
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... I ended up with the following command line solution using clustal omega which converts distance matrix to percent identity matrix:
clustalo-1.2.4-Ubuntu-x86_64 --full --percent-id --distmat-out=output.distmat -i input.aa.fa ...
written 7 months ago by
al-ash • 100
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