User: al-ash

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al-ash100
Reputation:
100
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Trusted
Location:
Japan/Okinawa/OIST
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2 days, 2 hours ago
Joined:
3 years, 8 months ago
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b*********@gmail.com

Posts by al-ash

<prev • 64 results • page 1 of 7 • next >
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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-ash100
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Comment: C: Generate all bifurkating newick trees given for N taxa
... 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-ash100
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Generate all possible bifurkating newick trees for N taxa
... 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 ...
generate tree newick written 9 weeks ago by al-ash100
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Comment: C: Combine node/branch labels from multiple trees into one
... 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-ash100
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Combine node/branch labels from multiple trees into one
... 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 ...
annotation label tree treegraph2 written 9 weeks ago by al-ash100
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Answer: A: yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
... 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-ash100
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Answer: A: Manual edit of multiple alignment
... 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-ash100
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Answer: A: Make matrix of protein pairwise identities/similarities from multiple protein se
... 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-ash100
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Comment: C: Platanus assembler : unable to start contig assembly, any problem with the comma
... 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-ash100
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Compare topologies of trees with non-identical tip labels
... 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 ...
R topology dendextend tanglegram tree written 7 months ago by al-ash100 • updated 7 months ago by jhc2.8k

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
Popular Question 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 17 months ago, created a question with more than 1,000 views. For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter 18 months ago, voted at least 25 times.

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