User: al-ash

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al-ash30
Reputation:
30
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New User
Location:
European Union
Last seen:
2 hours ago
Joined:
2 years, 12 months ago
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b*********@gmail.com

Posts by al-ash

<prev • 53 results • page 1 of 6 • next >
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Comment: C: BLAST, setting maximum number of hits
... (typo: should be -max_target_seqs instead of -max_target_seqns) ...
written 7 weeks ago by al-ash30
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Comment: C: Species tree vs Gene trees during evolutionary analyses: Does it matter?
... Did you reach any conclusion? If so, please share - this question is still missing an answer supported by some experience/evidence/literature reference. ...
written 8 weeks ago by al-ash30
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Answer: A: Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
... Concerning your 1st question (dS for each branch) - you can find it among the large amount of output information in the outfile (ENSGT00790000122969.mlc in your case) in a tabular form (in section labeled "dN & dS for each branch") and also as branch lengths of your tree in section "dS tree:". ...
written 8 weeks ago by al-ash30
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Comment: C: Unrooting Trees Help
... typo? `write.tree(unrooted_tr, "tree_unrooted.txt")` ...
written 9 weeks ago by al-ash30
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Comment: C: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
... While using your script again after some time I found that all the sequences for which retrieval fails ('Supplied id parameter is empty.'), are label in GenBank as "partial mRNA", i.e. not full CDS while it did not fail for any of my protein IDs for which there is a corresponding full mRNA in the da ...
written 11 weeks ago by al-ash30
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Comment: C: Make matrix of protein pairwise identities/similarities from multiple protein se
... You are right! Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) gives directly sequence %identity matrix (Result Summary -> Percent Identity Matrix in the web interface). ...
written 11 weeks ago by al-ash30
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Comment: C: Make matrix of protein pairwise identities/similarities from multiple protein se
... Not using Phylip before, I'm a bit confused by their documentation - according to http://evolution.genetics.washington.edu/phylip/doc/protdist.html the "program uses protein sequences" which would evoke to me, that the inout is multifasta, but actually it seems that the input is rather multiple alig ...
written 11 weeks ago by al-ash30
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Make matrix of protein pairwise identities/similarities from multiple protein sequences
... Is there an already existing tool to generate a matrix of pairwise protein identities/similarities for an input which consists of multiple protein sequences? I did not find a working solution for MAC OS/UNIX (the non-working solution for me is [MatGAT][1] for which I managed to find executables on ...
pairwise similarity protein identity matrix written 11 weeks ago by al-ash30 • updated 11 weeks ago by Bill Pearson800
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Answer: A: Tune criteria for extraction of consensus sequence from bam/sam alignment
... simple-consensus-per-read-group by Thomas Sibley is the tool I was looking for (https://github.com/MullinsLab/simple-consensus-per-read-group). It was recently updated so it can now correctly process BAMs with multiple scaffolds/contigs. ...
written 4 months ago by al-ash30
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Comment: C: Tune criteria for extraction of consensus sequence from bam/sam alignment
... Prakki, unfortunately I can't help you here since I was not testing the vcftools parametres. I did not yet manage to fine-tune the extraction of consensus, but as I wrote, that is mainly because I do not want to generate consensus which would have the nucleotide bases of reference at the position wh ...
written 4 months ago by al-ash30

Latest awards to al-ash

Popular Question 28 days 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 4 months ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Scholar 4 months ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Popular Question 8 months ago, created a question with more than 1,000 views. For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter 9 months ago, voted at least 25 times.

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