User: al-ash
al-ash • 100
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Posts by al-ash
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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 3 days 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 9 weeks 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 9 weeks 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 9 weeks 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 9 weeks 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 10 weeks 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 12 weeks 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 3 months ago by
al-ash • 100
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... In the example, they use `2> assemble.log` to redirect stderror to a file. In your original command you made a mistake by typing a space between `2` and `>`. That's why removing 2 helped. Alternatively, removing the space should fix this as well. ...
written 4 months ago by
al-ash • 100
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... I was using tanglegram() function from a great R package dendextend to draw comparison of phylogenetic trees. However, it requires to have identical set of tip labels in both trees and gives following error when presented with two trees with not identical set of tip labels:
Error in match_order ...
Latest awards to al-ash
Popular Question
9 days ago,
created a question with more than 1,000 views.
For How to append strings (from one file) to Fasta headers (in another file)
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: How to trim nucleotide sequences to length divisible by 3
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11 weeks ago,
created a question with more than 1,000 views.
For Entrez Direct E-utilities - using match and xtract to filter by data value
Popular Question
4 months ago,
created a question with more than 1,000 views.
For "Optimal" setting of CPU and max_memory in Trinity
Popular Question
8 months ago,
created a question with more than 1,000 views.
For How to append strings (from one file) to Fasta headers (in another file)
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Entrez Direct E-utilities - using match and xtract to filter by data value
Scholar
12 months ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
Scholar
13 months ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
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17 months ago,
created a question with more than 1,000 views.
For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
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